Pairwise Evolutionary Distances Research Articles

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences.

BackgroundThe estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The most accurate method is currently maximum likelihood over the entire triplet. However, this approach is relatively time consuming.ResultsWe show that an alternative estimator, based on pairwise estimates and therefore much faster to compute, has almost the same statistical power as the maximum likelihood estimator. We also provide a numerical approximation for its variance, which could otherwise only be estimated through an expensive re-sampling approach such as bootstrapping. An extensive simulation demonstrates that the approximation delivers precise confidence intervals. To illustrate the possible applications of these results, we show how they improve the detection of asymmetric evolution, and the identification of the closest relative to a given sequence in a group of homologs.ConclusionThe results presented in this paper constitute a basis for large-scale protein cross-comparisons of pairwise evolutionary distances.

Getting a Tree Fast: Neighbor Joining, FastME, and Distance‐Based Methods

Neighbor Joining (NJ), FastME, and other distance-based programs including BIONJ, WEIGHBOR, and (to some extent) FITCH, are fast methods to build phylogenetic trees. This makes them particularly effective for large-scale studies or for bootstrap analysis, which require runs on multiple data sets. Like maximum likelihood methods, distance methods are based on a sequence evolution model that is used to estimate the matrix of pairwise evolutionary distances. Computer simulations indicate that the topological accuracy of FastME is best, followed by FITCH, WEIGHBOR, and BIONJ, while NJ is worse. Moreover, FastME is even faster than NJ with large data sets. Best-distance methods are equivalent to parsimony in most cases, but become more accurate when the molecular clock is strongly violated or in the presence of long (e.g., outgroup) branches. This unit describes how to use distance-based methods, focusing on NJ (the most popular) and FastME (the most efficient today). It also describes how to estimate evolutionary distances from DNA and proteins, how to perform bootstrap analysis, and how to use CLUSTAL to compute both a sequence alignment and a phylogenetic tree.

RECONSTRUCTING AN ULTRAMETRIC GALLED PHYLOGENETIC NETWORK FROM A DISTANCE MATRIX

Given a distance matrix M that specifies the pairwise evolutionary distances between n species, the phylogenetic tree reconstruction problem asks for an edge-weighted phylogenetic tree that satisfies M, if one exists. We study some extensions of this problem to rooted phylogenetic networks. Our main result is an O(n(2) log n)-time algorithm for determining whether there is an ultrametric galled network that satisfies M, and if so, constructing one. In fact, if such an ultrametric galled network exists, our algorithm is guaranteed to construct one containing the minimum possible number of nodes with more than one parent (hybrid nodes). We also prove that finding a largest possible submatrix M' of M such that there exists an ultrametric galled network that satisfies M' is NP-hard. Furthermore, we show that given an incomplete distance matrix (i.e. where some matrix entries are missing), it is also NP-hard to determine whether there exists an ultrametric galled network which satisfies it.

Analysis of the overdispersed clock in the short-term evolution of hepatitis C virus: Using the E1/E2 gene sequences to infer infection dates in a single source outbreak.

The assumption of a molecular clock for dating events from sequence information is often frustrated by the presence of heterogeneity among evolutionary rates due, among other factors, to positively selected sites. In this work, our goal is to explore methods to estimate infection dates from sequence analysis. One such method, based on site stripping for clock detection, was proposed to unravel the clocklike molecular evolution in sequences showing high variability of evolutionary rates and in the presence of positive selection. Other alternatives imply accommodating heterogeneity in evolutionary rates at various levels, without eliminating any information from the data. Here we present the analysis of a data set of hepatitis C virus (HCV) sequences from 24 patients infected by a single individual with known dates of infection. We first used a simple criterion of relative substitution rate for site removal prior to a regression analysis. Time was regressed on maximum likelihood pairwise evolutionary distances between the sequences sampled from the source individual and infected patients. We show that it is indeed the fastest evolving sites that disturb the molecular clock and that these sites correspond to positively selected codons. The high computational efficiency of the regression analysis allowed us to compare the site-stripping scheme with random removal of sites. We demonstrate that removing the fast-evolving sites significantly increases the accuracy of estimation of infection times based on a single substitution rate. However, the time-of-infection estimations improved substantially when a more sophisticated and computationally demanding Bayesian method was used. This method was used with the same data set but keeping all the sequence positions in the analysis. Consequently, despite the distortion introduced by positive selection on evolutionary rates, it is possible to obtain quite accurate estimates of infection dates, a result of especial relevance for molecular epidemiology studies.

On the quality of tree-based protein classification

Phylogenetic analysis of protein sequences is widely used in protein function classification and delineation of subfamilies within larger families. In addition, the recent increase in the number of protein sequence entries with controlled vocabulary terms describing function (e.g. the Gene Ontology) suggests that it may be possible to overlay these terms onto phylogenetic trees to automatically locate functional divergence events in protein family evolution. Phylogenetic analysis of large datasets requires fast algorithms; and even 'fast', approximate distance matrix-based phylogenetic algorithms are slow on large datasets since they involve calculating maximum likelihood estimates of pairwise evolutionary distances. There have been many attempts to classify protein sequences on the family and subfamily level without reconstructing phylogenetic trees, but using hierarchical clustering with simpler distance measures, which also produce trees or dendrograms. How can these trees be compared in their ability to accurately classify protein sequences? Given a 'reference classification' or 'group membership labels' for a set of related protein sequences as well as a tree describing their relationships (e.g. a phylogenetic tree), we propose a method for dividing the tree into monophyletic or paraphyletic groups so as to optimize the correspondence between the reference groups and the tree-derived groups. We call the achieved optimal correspondence the 'accuracy of a tree-based classification (TBC)', which measures the ability of a tree to separate proteins of similar function into monophyletic or paraphyletic groups. We apply this measure to compare classical NJ and UPGMA phylogenetic trees with the trees obtained from hierarchical clustering using different protein similarity measures. Our preliminary analysis on a set of expert-curated protein families and alignments suggests that there is no uniformly superior algorithm, and that simple protein similarity measures combined with hierarchical clustering produce trees with reasonable and often the most accurate TBC. We used our measure to help us to design TIPS, a tree-building algorithm, based on agglomerative clustering with a similarity measure derived from profile scoring. TIPS is comparable with phylogenetic algorithms in terms of classification accuracy and is much faster on large protein families. Due to its time scalability and acceptable accuracy, TIPS is being used in the large-scale PANTHER protein classification project. The trees produced by different algorithms for different protein families can be viewed at http://panther.appliedbiosystems.com/pub/tree_quality/trees.jsp. For every tree and every level of classification granularity we provide the optimal TBC along with the reference classification. The script that evaluates the accuracy of TBC is available at http://panther.appliedbiosystems.com/pub/tree_quality/index.jsp

Variants of human papillomavirus types 53, 58 and 66 identified in Central Brazil.

The present study on molecular characterization of human papillomaviruses occurring in Central Brazil, describes two variants each of HPV-53 and HPV-58 and one variant of HPV-66 detected in samples from smears of women showing cervical intraepithelial neoplasia grade II (CIN II). Samples were assayed by PCR using MY09/ MY11 consensus primers, followed by restriction fragment length polymorphism typing. The five isolates showed atypical restriction fragment length profile and MY09/MY11 L1 PCR products were subsequently sequenced. Isolate Bsb-02 and Bsb-08 showed, respectively, 99% similarity to HPV-58 IS404 and 100% to HPV-58 IS417 previously described in the African Continent. Isolates Bsb-61 and Bsb-63 showed 98% similarity to HPV-53, and isolate Bsb-68, 97% similarity to HPV-66. Amino acid substitutions were found in two samples: one in Bsb-02 (T to N) at position 375 and the other in Bsb-61 (S to C) at position 343. Although all the substitutions in Bsb-68 proved to be silent, this sample showed the highest value of pairwise evolutionary distance (2.05%). In countries such as Brazil, where the virus prevalence is high and ethnicity, as well as socio-demographic characteristics, vary according to different regions, HPV variability must be wider and not yet clearly defined.

Molecular peculiarities of the lytA gene isolated from clinical pneumococcal strains that are bile insoluble.

The autolytic LytA amidase from 12 bile (deoxycholate)-insoluble streptococcal isolates (formerly classified as atypical Streptococcus pneumoniae) showing different antibiotic resistance patterns was studied. These atypical strains, which autolyze at the end of the stationary phase of growth, contain highly divergent lytA alleles (pairwise evolutionary distances of about 20%) compared to the lytA alleles of typical pneumococci. The atypical LytA amidases exhibit a peculiar deletion of two amino acids responsible for cell wall anchoring in the carboxy-terminal domain and have a reduced specific activity. These enzymes were inhibited by 1% deoxycholate but were activated by 1% Triton X-100, a detergent that could be used as an alternative diagnostic test for this kind of strain. Preparation of functional chimeric enzymes, PCR mutagenesis, and gene replacements demonstrated that the characteristic bile insolubility of these atypical strains was due to their peculiar carboxy-terminal domain and that the 2-amino-acid deletion was responsible for the inhibitory effect of deoxycholate. However, the deletion alone did not affect the specific activity of LytA. A detailed characterization of the genes encoding the 16S rRNA and SodA together with multilocus sequence typing indicated that the strains studied here are not a single clone and, although they cannot be strictly classified as typical pneumococci, they represent a quite diverse pool of organisms closely related to S. pneumoniae. The clinical importance of these findings is underlined by the role of the lytA gene in shaping the course of pneumococcal diseases. This study can also contribute to solving diagnostic problems and to understanding the evolution and pathogenic potential of species of the Streptococcus mitis group.

Genetic Diversity of Pestiviruses: Identification of Novel Groups and Implications for Classification

The complete Npro coding sequences were determined for 16 pestiviruses isolated from cattle, pig, and several wild ruminant species including reindeer, bison, deer, and bongo. Phylogenetic analysis enabled the segregation of pestiviruses into the established species bovine viral diarrhea virus-1 (BVDV-1), BVDV-2, border disease virus (BDV), and classical swine fever virus (CSFV). For BVDV-1 five distinct subgroups were identified, while BVDV-2, BDV, and CSFV were each subdivided into two subgroups. The virus isolates from bongo and deer as well as one porcine virus isolate belong to BVDV-1. Interestingly, the isolates from reindeer and bison are distinct from the established pestivirus species. The Npro sequences from these two viruses are more similar to BDV than to the other pestivirus species. Calculation of the pairwise evolutionary distances allowed a clear separation of the categories species, subgroup, and isolate only when the reindeer/bison viruses were considered as members of an additional pestivirus species. Furthermore, the entire E2 coding sequences of a representative set of virus isolates covering all recognized species and subgroups were studied. Segregation of pestiviruses based on the E2 region was identical with that obtained with the Npro sequences.

Higher Selection Pressure from Antiretroviral Drugs in Vivo Results in Increased Evolutionary Distance in HIV-1 pol

We investigated the effect of selection pressures on evolution of HIV-1 pol in 51 patients after switching to a new antiretroviral combination reverse transcriptase (RT) inhibitor therapy. Evolution of the protease (PR) and RT reading frames were analysed separately. Pairwise evolutionary distances (ED) were calculated between sequences from baseline and week 8 and between baseline and week 48 of protocol therapy. ED were calculated for all substitutions and for synonymous and nonsynonymous substitutions separately. At week 8 when HIV RNA reduction (selection pressure) was high, significantly more divergence in pol in both synonymous and nonsynonymous substitutions was found in patients with substantial RNA reduction (strong responders). Separate analyses of PR and RT revealed significantly greater ED in the RT (under selection pressure) of strong compared with nonresponders, whereas divergence between PR genes (not under selection pressure) did not differ in those two groups. Such differential evolution indicates that PR and RT were genetically unlinked and suggests recombination. The rapid increase of ED over the first 8 weeks was followed by only a minimal further rise by week 48, suggesting that selection of preexisting quasispecies accounted for the early changes. A disproportionally high number of synonymous substitutions accounted for the observed divergence and indicated that such genetic changes may not be completely silent.

Determination of Phylogenetic Relationships ofFlavobacterium psychrophilum(Flexibacter psychrophilus),Flavobacterium columnare(Flexibacter columnaris), andFlexibacter maritimusby Sequence Analysis of 16S Ribosomal RNA Genes Amplified by Polymerase Chain Reaction

The nearly complete small subunit 16S ribosomal RNA (rRNA) gene sequence amplified by polymerase chain reaction was determined for Flavobacterium psychrophilum (formerly Flexibacter psychrophilus) by using automated nucleotide sequencing. The sequence was found to be 1,465 base pairs (bp) in length, a size consistent with previously determined sequences for 14 other bacterial species from various taxa, including the yellow-pigmented bacteria. Sequence signatures confirmed that this organism was a member of the bacterial division Bacteroides–Flavobacterium. Parsimonious and additive phylogenetic trees were constructed with homology, and pairwise evolutionary distances were used to estimate phylogenetic relationships. Data show that F. psychrophilum, F. columnare, and Flexibacter maritimus are closely related, have a common descent, and represent a distinct group within the division Bacteroides–Flavobacterium. This group also included other organisms from the genera Flavobacterium and Cytophaga. Further, Flavobacterium aquatile, the type species for the genus Flavobacterium, was also determined to be a member of this “Flavobacterium–Cytophaga–Flexibacter subcomplex.” This supports previous assertions that the type strain of Flavobacterium should be changed to a more representative species such as Flavobacterium breve.