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PubMed2002

Evolutionary implications of phylogenetic analyses of the gene transfer agent (GTA) of Rhodobacter capsulatus.

The gene transfer agent (GTA) of the a-proteobacterium Rhodobacter capsulatus is a cell-controlled genetic exchange vector. Genes that encode the GTA structure are clustered in a 15-kb region of the R. capsulatus chromosome, and some of these genes show sequence similarity to known bacteriophage head and tail genes. However, the production of GTA is controlled at the level of transcription by a cellular two-component signal transduction system. This paper describes homologues of both the GTA structural gene cluster and the GTA regulatory genes in the a-proteobacteria Rhodopseudomonas palustris, Rhodobacter sphaeroides, Caulobacter crescentus, Agrobacterium tumefaciens and Brucella melitensis. These sequences were used in a phylogenetic tree approach to examine the evolutionary relationships of selected GTA proteins to these homologues and (pro)phage proteins, which was compared to a 16S rRNA tree. The data indicate that a GTA-like element was present in a single progenitor of the extant species that contain both GTA structural cluster and regulatory gene homologues. The evolutionary relationships of GTA structural proteins to (pro)phage proteins indicated by the phylogenetic tree patterns suggest a predominantly vertical descent of GTA-like sequences in the a-proteobacteria and little past gene exchange with (pro)phages.

Alphaproteobacteria↗
PubMed2002

Estimation of evolutionary parameters with phylogenetic trees.

An important issue in the phylogenetic analysis of nucleotide sequence data using the maximum likelihood (ML) method is the underlying evolutionary model employed. We consider the problem of simultaneously estimating the tree topology and the parameters in the underlying substitution model and of obtaining estimates of the standard errors of these parameter estimates. Given a fixed tree topology and corresponding set of branch lengths, the ML estimates of standard evolutionary model parameters are asymptotically efficient, in the sense that their joint distribution is asymptotically normal with the variance-covariance matrix given by the inverse of the Fisher information matrix. We propose a new estimate of this conditional variance based on estimation of the expected information using a Monte Carlo sampling (MCS) method. Simulations are used to compare this conditional variance estimate to the standard technique of using the observed information under a variety of experimental conditions. In the case in which one wishes to estimate simultaneously the tree and parameters, we provide a bootstrapping approach that can be used in conjunction with the MCS method to estimate the unconditional standard error. The methods developed are applied to a real data set consisting of 30 papillomavirus sequences. This overall method is easily incorporated into standard bootstrapping procedures to allow for proper variance estimation.

Animals↗
PubMed2004

Molecular evolutionary characterization of the mussel Mytilus histone multigene family: first record of a tandemly repeated unit of five histone genes containing an H1 subtype with "orphon" features.

The present work represents the first characterization of a clustered histone repetitive unit containing an H1 gene in a bivalve mollusk. To complete the knowledge on the evolutionary history of the histone multigene family in invertebrates, we undertake its characterization in five mussel Mytilus species, as an extension of our previous work on the H1 gene family. We report the quintet H4-H2B-H2A-H3-H1 as the major organization unit in the genome of Mytilus galloprovincialis with two 5S rRNA genes with interspersed nontranscribed spacer segments linked to the unit, which is not justified by their cotranscription with histone genes. Surprisingly, 3' UTR regions of histone genes show two different mRNA termination signals, a stem-loop and a polyadenylation signal, both related to the evolution of histone gene expression patterns throughout the cell cycle. The clustered H1 histones characterized share essential features with "orphon" H1 genes, suggesting a common evolutionary origin for both histone subtypes which is supported by the reconstructed phylogeny for H1 genes. The characterization of histone genes in four additional Mytilus species revealed the presence of strong purifying selection acting among the members of the family. The chromosomal location of most of the core histone genes studied was identified by FISH close to telomeric regions in M. galloprovincialis. Further analysis on nucleotide variation would be necessary to assess if H1 proteins evolve according to the birth-and-death model of evolution and if the effect of the strong purifying selection maintaining protein homogeneity could account for the homologies detected between clustered and "orphon" variants.

Amino Acid Sequence↗
PubMed2004

Isolation, characterization, and evolutionary divergence of mouse RNase 6: evidence for unusual evolution in rodents.

The evolution of the ribonuclease A (RNase A) vertebrate-specific enzyme family is interesting in that specific gene lineages appear to be responding to unique selective pressures in wildly diverse manners to generate proteins that are capable of reducing the infectivity of viruses, killing systemic pathogens, and inducing the growth of blood vessels all while maintaining the signature motifs of a ribonuclease. In this paper, we present the DNA sequence and gene structure of Mus musculus RNase 6 and examine the expression pattern and enzymatic activity of the recombinant protein. M. musculus RNase 6 has a limited expression pattern compared to human RNase 6 and is an efficient ribonuclease, with a catalytic efficiency 17-fold higher than that of human protein. Evolutionary analysis reveals that RNase 6 was subject to unusual evolutionary forces (dN/dS = 1.2) in an ancestral rodent lineage before the separation of Mus and Rattus. However, more recent evolution of rodent RNase 6 has been relatively conserved, with an average dN/dS of 0.66. These data suggest that the ancestral rodent RNase 6 was subject to accelerated evolution, resulting in the conserved modern gene, which most likely plays an important role in mouse physiology.

Amino Acid Sequence↗
PubMed2006

The evolutionary history of the transposable element Penelope in the Drosophila virilis group of species.

We have used phylogenetic techniques to study the evolutionary history of the Penelope transposable element in the Drosophila virilis species group. Two divergent types of Penelope have been detected, one previously described, clade I, and a new one which we have termed clade III. The phylogeny of some copies of the Penelope clade I element was partially consistent with the species phylogeny of the D. montana subphylad, suggesting cospeciation and allowing the estimation of the evolutionary rate of Penelope. Divergence times of elements found in different species are younger than the age of the species, suggesting horizontal transfer events.

Animals↗
PubMed2000

Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes.

The pairs of nitrogen fixation genes nifDK and nifEN encode for the alpha and beta subunits of nitrogenase and for the two subunits of the NifNE protein complex, involved in the biosynthesis of the FeMo cofactor, respectively. Comparative analysis of the amino acid sequences of the four NifD, NifK, NifE, and NifN in several archaeal and bacterial diazotrophs showed extensive sequence similarity between them, suggesting that their encoding genes constitute a novel paralogous gene family. We propose a two-step model to reconstruct the possible evolutionary history of the four genes. Accordingly, an ancestor gene gave rise, by an in-tandem paralogous duplication event followed by divergence, to an ancestral bicistronic operon; the latter, in turn, underwent a paralogous operon duplication event followed by evolutionary divergence leading to the ancestors of the present-day nifDK and nifEN operons. Both these paralogous duplication events very likely predated the appearance of the last universal common ancestor. The possible role of the ancestral gene and operon in nitrogen fixation is also discussed.

Dinitrogenase Reductase↗
PubMed2000

Efficiency of the neighbor-joining method in reconstructing deep and shallow evolutionary relationships in large phylogenies.

The neighbor-joining (NJ) method is widely used in reconstructing large phylogenies because of its computational speed and the high accuracy in phylogenetic inference as revealed in computer simulation studies. However, most computer simulation studies have quantified the overall performance of the NJ method in terms of the percentage of branches inferred correctly or the percentage of replications in which the correct tree is recovered. We have examined other aspects of its performance, such as the relative efficiency in correctly reconstructing shallow (close to the external branches of the tree) and deep branches in large phylogenies; the contribution of zero-length branches to topological errors in the inferred trees; and the influence of increasing the tree size (number of sequences), evolutionary rate, and sequence length on the efficiency of the NJ method. Results show that the correct reconstruction of deep branches is no more difficult than that of shallower branches. The presence of zero-length branches in realized trees contributes significantly to the overall error observed in the NJ tree, especially in large phylogenies or slowly evolving genes. Furthermore, the tree size does not influence the efficiency of NJ in reconstructing shallow and deep branches in our simulation study, in which the evolutionary process is assumed to be homogeneous in all lineages.

Computer Simulation↗
PubMed2000

An updated and comprehensive rRNA phylogeny of (crown) eukaryotes based on rate-calibrated evolutionary distances.

Recent experience with molecular phylogeny has shown that all molecular markers have strengths and weaknesses. Nonetheless, despite several notable discrepancies with phylogenies obtained from protein data, the merits of the small subunit ribosomal RNA (SSU rRNA) as a molecular phylogenetic marker remain indisputable. Over the last 10 to 15 years a massive SSU rRNA database has been gathered, including more then 3000 complete sequences from eukaryotes. This creates a huge computational challenge, which is exacerbated by phenomena such as extensive rate variation among sites in the molecule. A few years ago, a fast phylogenetic method was developed that takes into account among-site rate variation in the estimation of evolutionary distances. This "substitution rate calibration" (SRC) method not only corrects for a major source of artifacts in phylogeny reconstruction but, because it is based on a distance approach, allows comprehensive trees including thousands of sequences to be constructed in a reasonable amount of time. In this study, a nucleotide variability map and a phylogenetic tree were constructed, using the SRC method, based on all available (January 2000) complete SSU rRNA sequences (2551) for species belonging to the so-called eukaryotic crown. The resulting phylogeny constitutes the most complete description of overall eukaryote diversity and relationships to date. Furthermore, branch lengths estimated with the SRC method better reflect the huge differences in evolutionary rates among and within eukaryotic lineages. The ribosomal RNA tree is compared with a recent protein phylogeny obtained from concatenated actin, alpha-tubulin, beta-tubulin, and elongation factor 1-alpha amino acid sequences. A consensus phylogeny of the eukaryotic crown based on currently available molecular data is discussed, as well as specific problems encountered in analyzing sequences when large differences in substitution rate are present, either between different sequences (rate variation among lineages) or between different positions within the same sequence (among-site rate variation).

Base Sequence↗
PubMed2000

Evolutionary lability of context-dependent codon bias in bacteria.

In bacteria, synonymous codon usage can be considerably affected by base composition at neighboring sites. Such context-dependent biases may be caused by either selection against specific nucleotide motifs or context-dependent mutation biases. Here we consider the evolutionary conservation of context-dependent codon bias across 11 completely sequenced bacterial genomes. In particular, we focus on two contextual biases previously identified in Escherichia coli; the avoidance of out-of-frame stop codons and AGG motifs. By identifying homologues of E. coli genes, we also investigate the effect of gene expression level in Haemophilus influenzae and Mycoplasma genitalium. We find that while context-dependent codon biases are widespread in bacteria, few are conserved across all species considered. Avoidance of out-of-frame stop codons does not apply to all stop codons or amino acids in E. coli, does not hold for different species, does not increase with gene expression level, and is not relaxed in Mycoplasma spp., in which the canonical stop codon, TGA, is recognized as tryptophan. Avoidance of AGG motifs shows some evolutionary conservation and increases with gene expression level in E. coli, suggestive of the action of selection, but the cause of the bias differs between species. These results demonstrate that strong context-dependent forces, both selective and mutational, operate on synonymous codon usage but that these differ considerably between genomes.

Codon↗
PubMed2005

Bounding the number of hybridisation events for a consistent evolutionary history.

Evolutionary processes such as hybridisation, lateral gene transfer, and recombination are all key factors in shaping the structure of genes and genomes. However, since such processes are not always best represented by trees, there is now considerable interest in using more general networks instead. For example, in recent studies it has been shown that networks can be used to provide lower bounds on the number of recombination events and also for the number of lateral gene transfers that took place in the evolutionary history of a set of molecular sequences. In this paper we describe the theoretical performance of some related bounds that result when merging pairs of trees into networks.

Evolution, Molecular↗
PubMed1999

Evolutionary adaptations of cochlear function in Jamaican mormoopid bats.

Mormoopid bat species have their echolocation system adapted to different hunting strategies. To study the corresponding mechanical properties of their inner ear, we measured distortion-product otoacoustic emissions to assess cochlear sensitivity and tuning. Mormoops blainvillii, Pteronotus macleayii and P. quadridens use frequency-modulated echolocation signals, sometimes preceded by a short narrowband signal component. Their distortion-product otoacoustic emission-threshold curves are most sensitive between 30 and 50 kHz and show no adaptation to the narrowband echolocation components. In contrast, the constant-frequency bat P. parnellii always uses long constant-frequency call components. Its inner ear is maximally sensitive at 62 kHz, the echo-frequency of the dominant constant-frequency component, and pronounced insensitivities at 61 and 93 kHz (CF2 and CF3 call frequency) are the major evolutionary change in comparison to its relatives. Furthermore, in P. parnellii, the optimum cochlear frequency separation is minimal at 62 and 93 kHz, associated with enhanced cochlear tuning, while for the other mormoopids there is no indication of enhanced tuning. The phylogeny of mormoopids, assessed by mitochondrial DNA analysis, shows a close relationship between the Pteronotus species. This suggests that major cochlear redesign, associated with the acquisition of echolocation-call specific cochlear processing in P. parnellii, has occurred within a relatively short evolutionary time scale.

Acoustic Stimulation↗
PubMed2001

The evolutionary life history of P transposons: from horizontal invaders to domesticated neogenes.

P elements, a family of DNA transposons, are known as aggressive intruders into the hitherto uninfected gene pool of Drosophila melanogaster. Invading through horizontal transmission from an external source they managed to spread rapidly through natural populations within a few decades. Owing to their propensity for rapid propagation within genomes as well as within populations, they are considered as the classic example of selfish DNA, causing havoc in a genomic environment permissive for transpositional activity. Tracing the fate of P transposons on an evolutionary scale we describe different stages in their evolutionary life history. Starting from horizontal transfer events, which now appear to be rather a common phenomenon, the initial transpositional burst in the new host is slowed down by the accumulation of defective copies as well as host-directed epigenetic silencing. This leads to the loss of mobility and, finally, to molecular erosion by random mutations. Possible escape routes from genomic extinction are the reactivation within the original host genome by recombination or suspension of the repressing regime, horizontal emigration to a virgin gene pool, or genomic integration and acquisition of a novel function as a domesticated host gene.

Animals↗
PubMed1998

Evolutionary changes in sites and timing of actin gene expression in embryos of the direct- and indirect-developing sea urchins, Heliocidaris erythrogramma and H. tuberculata.

We describe an evolutionary comparison of expression of the actin gene families of two congeneric sea urchins. Heliocidaris tuberculata develops indirectly via a planktonic feeding pluteus that forms a juvenile rudiment after a long period of larval development. H. erythrogramma is a direct developer that initiates formation of a juvenile rudiment immediately following gastrulation. The developmental expression of each actin isoform of both species was determined by in situ hybridization. The observed expression patterns are compared with known expression patterns in a related indirect-developing sea urchin, Strongylocentrotus purpuratus. Comparisons reveal unexpected patterns of conserved and divergent expression. Cytoplasmic actin, CyIII, is expressed in the aboral ectoderm cells of the indirect developers, but is an unexpressed pseudogene in H. erythrogramma, which lacks aboral ectoderm. This change is correlated with developmental mode. Two CyII actins are expressed in S. purpuratus, and one in H. erythrogramma, but no CyII is expressed in H. tuberculata despite its great developmental similarity to S. purpuratus. CyI expression differs slightly between Heliocidaris and Strongylocentrotus with more ectodermal expression in Heliocidaris. Evolutionary changes in actin gene expression reflect both evolution of developmental mode as well as a surprising flexibility in gene expression within a developmental mode.

Actins↗
PubMed2004

Association between evolutionary history of angiotensinogen haplotypes and plasma levels.

Over the last decade, considerable effort has been invested in studying the associations between angiotensinogen (AGT) variants, AGT plasma levels and high blood pressure. Evidence accumulated to date consistently supports the relationship between the AGT locus and the protein level, while an influence on blood pressure has been difficult to establish; in both instances the predisposing molecular variants are not fully defined. An evolutionary approach, taking into account the phylogenetic relationship between all the polymorphisms at this locus, may improve our understanding of the genetic nature of these quantitative phenotypes. Accordingly we sequenced a 6.8 kb region of the AGT gene in 57 Nigerian individuals (29 with high AGT plasma levels and 28 with low AGT plasma levels). Haplotypes were grouped into seven major haplogroups and their phylogenetic relationship was established. The association between haplogroups and AGT plasma levels was investigated. A significant linear correlation was detected between haplogroup genetic distance and AGT levels, suggesting a nonrandom accumulation of risk-associated mutations during the evolutionary history of the AGT gene.

Angiotensinogen↗
PubMed2004

Liquid-feeding performances of ants (Formicidae): ecological and evolutionary implications.

Disparities in liquid-feeding performances of major ant taxa have likely been important to resource partitioning among ants, to the nature and composition of ant partnerships with plants and sap-feeding trophobionts, and to ecological and evolutionary diversification of ant taxa. We measured performance volumetrically for individual workers of 77 ant species from lowland rain forests of Amazonia and Borneo and three key North American taxa. In trials with 9% sucrose solution, performances were strongly related to body size (and alitrunk length) and to proventricular structure at generic to subfamilial levels. Highly modified proventriculi were associated with disproportionately large load sizes in Formicinae and certain small-bodied Dolichoderinae. These same taxa also ingested liquids more rapidly during foraging than did similar-sized species with plesiomorphic proventriculi. Secondarily reduced foraging performances of several formicines likely reflect ecological or evolutionary trade-offs related to dietary specialization or anti-predator defenses. Across formicines and dolichoderines, performances differed by functional group. Relatively small loads and slow uptake characterized species tending trophobionts (mainly Hemiptera) day and night in large worker aggregations. Large loads and rapid uptake typified solitary, diurnal "leaf-foragers." Intermediate feeding performances characterized a few species that both tended trophobionts in small aggregates and frequently foraged alone.

Animals↗
PubMed2006

The narrow-leaf syndrome: a functional and evolutionary approach to the form of fog-harvesting rosette plants.

Plants that use fog as an important water-source frequently have a rosette growth habit. The performance of this morphology in relation to fog interception has not been studied. Some first-principles from physics predict that narrow leaves, together with other ancillary traits (large number and high flexibility of leaves, caudices, and/or epiphytism) which constitute the "narrow-leaf syndrome" should increase fog-interception efficiency. This was tested using aluminum models of rosettes that differed in leaf length, width and number and were exposed to artificial fog. The results were validated using seven species of Tillandsia and four species of xerophytic rosettes. The total amount of fog intercepted in rosette plants increased with total leaf area, while narrow leaves maximized interception efficiency (measured as interception per unit area). The number of leaves in the rosettes is physically constrained because wide-leafed plants can only have a few blades. At the limits of this constraint, net fog interception was independent of leaf form, but interception efficiency was maximized by large numbers of narrow leaves. Atmospheric Tillandsia species show the narrow-leaf syndrome. Their fog interception efficiencies were correlated to the ones predicted from aluminum-model data. In the larger xerophytic rosette species, the interception efficiency was greatest in plants showing the narrow-leaf syndrome. The adaptation to fog-harvesting in several narrow-leaved rosettes was tested for evolutionary convergence in 30 xerophytic rosette species using a comparative method. There was a significant evolutionary tendency towards the development of the narrow-leaf syndrome the closer the species grew to areas where fog is frequently available. This study establishes convergence in a very wide group of plants encompassing genera as contrasting as Tillandsia and Agave as a result of their dependence on fog.

Aluminum↗
PubMed2006

Evolutionary dynamics of olfactory and other chemosensory receptor genes in vertebrates.

The numbers of functional olfactory receptor (OR) genes in humans and mice are about 400 and 1,000 respectively. In both humans and mice, these genes exist as genomic clusters and are scattered over almost all chromosomes. The difference in the number of genes between the two species is apparently caused by massive inactivation of OR genes in the human lineage and a substantial increase of OR genes in the mouse lineage after the human-mouse divergence. Compared with mammals, fishes have a much smaller number of OR genes. However, the OR gene family in fishes is much more divergent than that in mammals. Fishes have many different groups of genes that are absent in mammals, suggesting that the mammalian OR gene family is characterized by the loss of many group genes that existed in the ancestor of vertebrates and the subsequent expansion of specific groups of genes. Therefore, this gene family apparently changed dynamically depending on the evolutionary lineage and evolved under the birth-and-death model of evolution. Study of the evolutionary changes of two gene families for vomeronasal receptors and two gene families for taste receptors, which are structurally similar, but remotely related to OR genes, showed that some of the gene families evolved in the same fashion as the OR gene family. It appears that the number and types of genes in chemosensory receptor gene families have evolved in response to environmental needs, but they are also affected by fortuitous factors.

Animals↗
PubMed2006

Diversity of secondary endosymbiont-derived actin-coding genes in cryptomonads and their evolutionary implications.

In the secondary endosymbiotic organisms of cryptomonads, the symbiont actin genes have been found together with the host one. To examine whether they are commonly conserved and where they are encoded, host and symbiont actin genes from Pyrenomonas helgolandii were isolated, and their specific and homologous regions were digoxigenin (DIG) labeled separately. Using these probes, Southern hybridization was performed on 13 species of cryptomonads. They were divided into three groups: (1) both host and symbiont actin gene signals were detected, (2) only the host actin gene signal was detected, and (3) host and unknown actin signals were detected. The phylogenetic analysis of these actin gene sequences indicated that the evolutionary rates of the symbiont actin genes were accelerated more than those of the hosts. The unknown actin signals were recognized as the highly diverged symbiont actin genes. One of the diverged symbiont actin sequences from Guillardia theta is presumed to be as a pseudogene or to its precursor. Southern hybridizations based on the samples divided by pulsed-field gel electrophoresis showed that all actin genes were encoded by the host nuclei. These results possibly represent the evolutionary fate of the symbiont actin gene in cryptomonads, which was firstly transferred from the symbiont nucleus or nucleomorph, to the host nucleus and became a pseudogene and then finally disappeared there.

Actins↗