Molecular Biology and Evolution

Base pairing constraints drive structural epistasis in ribosomal RNA sequences.

Publication Date: 2010 Mar 8 PMID: 20211929
Authors: Dutheil, J. Y. - Jossinet, F. - Westhof, E.
Journal: Mol Biol Evol

It has long been accepted that the structural constraints stemming from the three-dimensional structure of ribosomal RNA lead to coevolution through compensating mutations between interacting sites. State-of-the-art methods for detecting coevolving sites, however, while reaching high levels of specificity and sensitivity for Watson-Crick (WC) pairs of the helices defining the secondary structure, only scarcely reveal tertiary interactions occuring at the level of the three-dimensional structure. In order to understand the relative failure of coevolutionary methods to detect such interactions, we analyze 2,682 interacting sites derived from high resolution structures, which include a comprehensive data set of rRNA sequences from Archaea and Bacteria. We report a striking difference in the amount of coevolution between WC and non-WC pairs. In order to understand this pattern, we derive fitness landscapes from the geometry of base pairing interactions and construct neutral networks of substitutions for each type of interaction. These networks show that coevolution is a property of WC pairs because, unlike non-WC pairs, their landscapes exhibit fitness valleys, a single mutation in a WC pair resulting in a fitness drop. Secondly, we used the inferred neutral networks to estimate the level of constraint acting on each type of base pair and show that it correlates negatively with the observed rate of substitutions for all non-WC pairs. WC-pairs appear as outliers, fixing more substitutions than expected according to their level of constraint. We here propose that the rate of substitution in WC pairs is due to coevolution resulting from constraints acting at intermediate levels of organization, namely the one of the helical stem with its forming WC-pairs. In agreement with this hypothesis, we report a significant excess of intra-helical, inter-WC-pair coevolution compared to inter-helices pairs. Altogether, these results show that detailed biochemical knowledge is required and has to be incorporated into evolutionary reasoning in order to understand the fine patterns of variation at the molecular level. They also demonstrate that coevolutionary analysis provides almost exclusively two-dimensional information and only little three-dimensional signal.

post to: CiteULike

An alignment confidence score capturing robustness to guide-tree uncertainty.

Publication Date: 2010 Mar 5 PMID: 20207713
Authors: Penn, O. - Privman, E. - Landan, G. - Graur, D. - Pupko, T.
Journal: Mol Biol Evol

Multiple sequence alignment (MSA) is the basis for a wide range of comparative sequence analyses, from molecular phylogenetics to three-dimensional structure prediction. Sophisticated algorithms have been developed for sequence alignment, but in practice, many errors can be expected and extensive portions of the MSA are unreliable. Hence, it is imperative to understand and characterize the various sources of errors in MSAs, and to quantify site-specific alignment confidence. In this paper we show that uncertainties in the guide tree used by progressive alignment methods are a major source of alignment uncertainty. We use this insight to develop a novel method for quantifying the robustness of each alignment column to guide-tree uncertainty. We build on the widely used bootstrap method for perturbing the phylogenetic tree. Specifically, we generate a collection of trees and use each as a guide tree in the alignment algorithm, thus producing a set of MSAs. We next test the consistency of every column of the MSA obtained from the unperturbed guide tree with respect to the set of MSAs. We name this measure the "GUIDe tree based AligNment ConfidencE" (GUIDANCE) score. Using the BAliBASE benchmark as well as simulation studies, we show that GUIDANCE scores accurately identify errors in MSAs. Additionally, we compare our results to the previously published Heads-or-Tails (HoT) score, and show that the GUIDANCE score is a better predictor of unreliably aligned regions.

post to: CiteULike

Major East-West Division Underlies Y Chromosome Stratification Across Indonesia.

Publication Date: 2010 Mar 5 PMID: 20207712
Authors: Karafet, T. M. - Hallmark, B. - Cox, M. P. - Sudoyo, H. - Downey, S. - Lansing, J. S. - Hammer, M. F.
Journal: Mol Biol Evol

The early history of Island Southeast Asia is often characterized as the story of two major population dispersals: the initial Paleolithic colonization of Sahul approximately 45 thousand years ago and the much later Neolithic expansion of Austronesian-speaking farmers approximately 4,000 years ago. Here, in the largest survey of Indonesian Y chromosomes to date, we present evidence for multiple genetic strata that likely arose through a series of distinct migratory processes. We genotype an extensive battery of Y chromosome markers, including 85 SNPs/indels and 12 Y-STRs, in a sample of 1,917 men from 32 communities located across Indonesia. We find that the paternal gene pool is sharply subdivided between western and eastern locations, with a boundary running between the islands of Bali and Flores. Analysis of molecular variance reveals one of the highest levels of between-group variance yet reported for human Y chromosome data (e.g., ?ST = 0.47). Eastern Y chromosome haplogroups are closely related to Melanesian lineages (i.e., within the C, M and S subclades) and likely reflect the initial wave of colonization of the region, while the majority of western Y chromosomes (i.e., O-M119*, O-P203, and O-M95*) are related to haplogroups that may have entered Indonesia during the Paleolithic from mainland Asia. In addition, two novel markers (P201, P203) provide significantly enhanced phylogenetic resolution of two key haplogroups (O-M122, O-M119) that are often associated with the Austronesian expansion. This more refined picture leads us to put forward a four-phase colonization model in which Paleolithic migrations of hunter-gatherers shape the primary structure of current Indonesian Y chromosome diversity, and Neolithic incursions make only a minor impact on the paternal gene pool, despite the large cultural impact of the Austronesian expansion.

post to: CiteULike

Parallelism in evolution of highly repetitive DNAs in sibling species.

Publication Date: 2010 Mar 4 PMID: 20203289
Authors: Mravinac, B. - Plohl, M.
Journal: Mol Biol Evol

Characterization of heterochromatin in the flour beetle Tribolium audax revealed two highly repetitive DNA families, TAUD1 and TAUD2, which together constitute almost 60% of the whole genome. Both families originated from a common ancestral approximately 110 bp repeating unit. Tandem arrangement of these elements in TAUD1 is typical for satellite DNAs, while TAUD2 represents a dispersed family based on 1412 bp complex higher-order repeats composed of inversely oriented approximately 110 bp units. Comparison with repetitive DNAs in the sibling species T. madens showed similarities in nucleotide sequence and length of basic repeating units and also revealed structural and organizational parallelism in tandem and dispersed families assembled from these elements. In both Tribolium species, one tandem and one dispersed family build equivalent distribution patterns in the pericentromeric heterochromatin of all chromosomes including supernumeraries. Differences in the nucleotide sequence and in the complexity of higher-order structures between families of the same type suggest a scenario according to which rearranged variants of the corresponding ancestral families were formed and distributed in genomes during or after the speciation event, following the same principles independently in each descendant species. We assume that random effects of sequence dynamics should be constrained by organizational and structural features of repeating units and possible requirements for spatial distribution of particular sequence elements. An interspersed pattern of repetitive families also points to the intensive recombination events in heterochromatin. Synergy between the meiotic bouquet stage and satellite DNA sequence dynamics could make a positive feed-back loop that promotes the observed genome-wide distribution. At the same time, considering the abundance of these DNAs in heterochromatin spanning the (peri)centromeric chromosomal segments, we speculate that diverged repetitive sequences might represent the DNA basis of reproductive barrier between the two sibling species.

post to: CiteULike

Phylogeography takes a relaxed random walk in continuous space and time.

Publication Date: 2010 Mar 4 PMID: 20203288
Authors: Lemey, P. - Rambaut, A. - Welch, J. J. - Suchard, M. A.
Journal: Mol Biol Evol

Research aimed at understanding the geographic context of evolutionary histories is burgeoning across biological disciplines. Recent endeavors attempt to interpret contemporaneous genetic variation in the light of increasingly detailed geographical and environmental observations. Such interest has promoted the development of phylogeographic inference techniques that explicitly aim to integrate such heterogeneous data. One promising development involves reconstructing phylogeographic history on a continuous landscape. Here, we present a Bayesian statistical approach to infer continuous phylogeographic diffusion using random walk models while simultaneously reconstructing the evolutionary history in time from molecular sequence data. Moreover, by accommodating branch-specific variation in dispersal rates, we relax the most restrictive assumption of the standard Brownian diffusion process and demonstrate increased statistical efficiency in spatial reconstructions of over-dispersed random walks by analyzing both simulated and real viral genetic data. We further illustrate how drawing inference about summary statistics from a fully-specified stochastic process over both sequence evolution and spatial movement reveals important characteristics of a rabies epidemic. Together with recent advances in discrete phylogeographic inference, the continuous model developments furnish a flexible statistical framework for biogeographical reconstructions that is easily expanded upon to accommodate various landscape genetic features.

post to: CiteULike

Copy Number Changes of CNV Regions in Intersubspecific Crosses of the House Mouse.

Publication Date: 2010 Mar 3 PMID: 20200126
Authors: Scavetta, R. J. - Tautz, D.
Journal: Mol Biol Evol

Copy number variation (CNV) contributes significantly to natural genetic variation within and between populations. However, the mutational mechanisms leading to copy number variation, as well as the processes that control the size of CNV regions are so far not well understood. Here we have analysed a gene family that forms CNV regions on the X- and the Y-chromosomes in Mus musculus. These CNV regions show copy number differences in two subspecies, M. m. domesticus and M. m. musculus. Assessment of copy numbers at these loci for individuals caught in a natural hybrid zone showed copy number increases and a large variance among individuals. Crosses of natural hybrid animals among each other produced even more extreme variants with major differences in copy number in the offspring from the same parents. To assess the inheritance pattern of the loci further, we have produced F1 and backcross hybrid animals from these subspecies. We found that copy number expansions can already be traced in F1 offspring and they became stronger in the backcross individuals. Specific analysis of hybrid male offspring indicated that neither meiotic recombination nor inter-chromosomal exchange was required for creating these changes, since the X- and Y-chromosome have no homologues in males. This suggests that intrachromosomal exchanges can drive copy number variation and that this can occur at an elevated frequency in interspecific crosses, even within an individual. Accordingly, we find copy number mosaicism in individuals, i.e. DNA from different tissues of the same individual can have different copy numbers for the loci studied. A preliminary survey of autosomal loci suggests that these can also be subject to change in hybrids. Hence, we conclude that the effects we see are not only restricted to some specific loci and that they may be caused by a general induction of replication coupled repair-processes.

post to: CiteULike

Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size.

Publication Date: 2010 Mar 1 PMID: 20194429
Authors: Slotte, T. - Foxe, J. P. - Hazzouri, K. M. - Wright, S. I.
Journal: Mol Biol Evol

Recent studies comparing genome-wide polymorphism and divergence in Drosophila have found evidence for a surprisingly high proportion of adaptive amino acid fixations, but results for other taxa are mixed. In particular, few studies have found convincing evidence for adaptive amino acid substitution in plants. To assess the generality of this finding, we have sequenced 257 loci in the outcrossing crucifer Capsella grandiflora, which has a large effective population size and low population structure. Using a new method that jointly infers selective and demographic effects, we estimate that 40% of amino acid substitutions were fixed by positive selection in this species, and we also infer a low proportion of slightly deleterious amino acid mutations. We contrast these estimates with those for a similar dataset from the closely related Arabidopsis thaliana and find significantly higher rates of adaptive evolution, and fewer nearly neutral mutations in C. grandiflora. In agreement with results for other taxa, genes involved in reproduction show the strongest evidence for positive selection in C. grandiflora. Taken together these results imply that both positive and purifying selection are more effective in C. grandiflora than in A. thaliana, consistent with the contrasting demographic history and effective population sizes of these species.

post to: CiteULike

Rooting the Ribosomal Tree of Life.

Publication Date: 2010 Mar 1 PMID: 20194428
Authors: Fournier, G. P. - Gogarten, J. P.
Journal: Mol Biol Evol

The origin of the genetic code and the rooting of the tree of life are two of the most challenging problems in the study of life's early evolution. Although both have been the focus of numerous investigations utilizing a variety of methods, until now each problem has been addressed independently. Typically, attempts to root the tree of life have relied on phylogenies of genes with ancient duplications, which are subject to artifacts of tree reconstruction and horizontal gene transfer, or specific physiological characters believed to be primitive, which are often based on subjective criteria. Here, we demonstrate a unique method for rooting based on the identification of amino acid usage biases comprising the residual signature of a more primitive genetic code. Using a phylogenetic tree of concatenated ribosomal proteins, our analysis of amino acid compositional bias detects a strong and unique signal associated with the early expansion of the genetic code, placing the root of the translation machinery along the bacterial branch.

post to: CiteULike

Phylogenomic evidence for separate acquisition of plastids in cryptophytes, haptophytes and stramenopiles.

Publication Date: 2010 Mar 1 PMID: 20194427
Authors: Baurain, D. - Brinkmann, H. - Petersen, J. - Rodriguez-Ezpeleta, N. - Stechmann, A. - Demoulin, V. - Roger, A. J. - Burger, G. - Lang, B. F. - Philippe, H.
Journal: Mol Biol Evol

According to the chromalveolate hypothesis (Cavalier-Smith 1999, J Eukaryot Microbiol 46:347-366), the four eukaryotic groups with chlorophyll c-containing plastids originate from a single photosynthetic ancestor, which acquired its plastids by secondary endosymbiosis with a red alga. So far, molecular phylogenies have failed to either support or disprove this view. Here we devise a phylogenomic falsification of the chromalveolate hypothesis that estimates signal strength across the three genomic compartments: if the four chlorophyll c-containing lineages indeed derive from a single photosynthetic ancestor, then similar amounts of plastid, mitochondrial and nuclear sequences should allow to recover their monophyly. Our results refute this prediction, with statistical support levels too different to be explained by evolutionary rate variation, phylogenetic artifacts, or endosymbiotic gene transfer. Therefore, we reject the chromalveolate hypothesis as falsified in favor of more complex evolutionary scenarios involving multiple higher-order eukaryote-eukaryote endosymbioses.

post to: CiteULike

Birth-and-death long-term evolution promotes histone H2B variant diversification in the male germinal cell line.

Publication Date: 2010 Mar 1 PMID: 20194426
Authors: Gonzalez-Romero, R. - Rivera-Casas, C. - Ausio, J. - Mendez, J. - Eirin-Lopez, J. M.
Journal: Mol Biol Evol

The rich diversity within each of the five histone families (H1, H2A, H2B, H3, H4) can hardly be reconciled with the notion of homogenizing evolution. The prevalence of birth-and-death long-term evolution over concerted evolution has already been demonstrated in the linker histone H1 family as well as for the H2A, H3 and H4 core histone families. However, information about histone H2B is lacking. In the present work we have analyzed the diversity of the members of this histone family across different eukaryotic genomes and have characterized the mechanisms involved in their long-term evolution. Our results reveal that, quite in contrast with other histones, H2B variants are subject to a very rapid process of diversification which primarily affects the male germinal cell lineage and involves their functional specialization probably as a consequence of neofunctionalization and subfunctionalization events after gene duplication. The overall parallelism observed between the molecular phylogenies and the relationships among the electrostatic potentials of the different variants suggests that the latter may have played a major structural selective constraint during H2B evolution. It thus seems that the reorganization of chromatin structure during spermiogenesis might have affected the evolutionary constraints driving histone H2B evolution, leading to an increase in diversity.

post to: CiteULike

Structural considerations in the fitness landscape of a virus.

Publication Date: 2010 Mar 1 PMID: 20194425
Authors: Watabe, T. - Kishino, H.
Journal: Mol Biol Evol

Viral fitness is determined by replication within-hosts and transmission between them. We examine how pleiotropic mutations that have antagonistic effects (i.e., antibody evasion versus receptor binding) on viral replication within hosts can impact viral immune escape in the host population. When the host population is vaccinated, the virus escapes from passive immunity by mutations in the antibody-binding region on the surface of the target protein. However, the reduced ability of the antibody to bind the virus is often accompanied by a reduced ability of the virus to bind the cell receptor, because the antibody-binding region overlaps with the receptor-binding domain. The types of permitted mutations are limited. To investigate the causal relation between a mutation in a viral genome and adaptive evolution of a viral population, we developed a mathematical model that describes the population dynamics of viruses, antibodies and normal/infected cells within a host. The coefficients describe the binding affinity between the virus and the induced antibody and that between the virus and its receptor. Our knowledge-based index enables us to estimate the effect of a mutation in a binding region on the binding affinity. Using population genetic theory, we evaluated the probability that a mutant is fixed in a host population. The mutations which can be fixed with high probabilities may determine how long a vaccine remains effective. We simulate the adaptive evolution of coronavirus, the etiological agent of severe acute respiratory syndrome, and show that some of mutations in the receptor-binding domain may have high fixation probabilities in the vaccinated host population.

post to: CiteULike

Bayesian estimation of divergence times from large sequence alignments.

Publication Date: 2010 Mar 1 PMID: 20194424
Authors: Guindon, S.
Journal: Mol Biol Evol

Bayesian estimation of divergence times from molecular sequences relies on sophisticated Markov Chain Monte Carlo techniques and Metropolis-Hastings samplers have been successfully used in that context. This approach involves heavy computational burdens which can hinder the analysis of large phylogenomic data sets. Reliable estimation of divergence times can also be extremely time-consuming, if not impossible, for sequence alignments that convey weak or conflicting phylogenetic signals, emphasizing the need for more efficient sampling methods. This article describes a new approach that estimates the posterior density of substitution rates and node times. The prior distribution of rates accounts for their potential autocorrelation along lineages while priors on node ages are modelled with uniform densities. Also, the likelihood function is approximated by a multivariate normal density. The combination of these components leads to convenient mathematical simplifications, allowing the posterior distribution of rates and times to be estimated using a Gibbs sampling algorithm. The analysis of four real-world data sets shows that this sampler outperforms the standard Metropolis-Hastings approach and demonstrates the suitability of this new method for analysing large and/or difficult data sets.

post to: CiteULike

Gene family size conservation is a good indicator of evolutionary rates.

Publication Date: 2010 Mar 1 PMID: 20194423
Authors: Chen, F. C. - Chen, C. J. - Li, W. H. - Chuang, T. J.
Journal: Mol Biol Evol

The evolution of duplicate genes has been a topic of broad interest. Here we propose that the conservation of gene family size is a good indicator of the rate of sequence evolution and some other biological properties. By comparing the human-chimpanzee-macaque orthologous gene families with and without family size conservation, we demonstrate that genes of family-size-conserved families evolve more slowly than those of non-family-size-conserved families. Our results further demonstrate that both family expansion and contraction events may accelerate gene evolution, resulting in elevated evolutionary rates in the non-family-size-conserved families. In addition, we show that the duplicate genes with family size conservation evolve significantly more slowly than those without family size conservation. Interestingly, the median evolutionary rate of singletons falls in between those of the above two types of duplicate gene families. Our results thus suggest that the controversy on whether duplicate genes evolve more slowly than singletons can be resolved when family size conservation is taken into consideration. Furthermore, we also observe that duplicate genes with family size conservation have the highest level of gene expression/expression breadth, the highest proportion of essential genes and the lowest gene compactness, followed by singletons, and then by duplicate genes without family size conservation. Such a trend accords well with our observations of evolutionary rates. Our results thus point to the importance of family size conservation in the evolution of duplicate genes.

post to: CiteULike

Extensive Divergence in Alternative Splicing Patterns After Gene and Genome Duplication During the Evolutionary History of Arabidopsis.

Publication Date: 2010 Feb 25 PMID: 20185454
Authors: Zhang, P. G. - Huang, S. Z. - Pin, A. L. - Adams, K. L.
Journal: Mol Biol Evol

Gene duplication at various scales, from single gene duplication to whole genome duplication, has occurred throughout eukaryotic evolution and contributed greatly to the large number of duplicated genes in the genomes of many eukaryotes. Previous studies have shown divergence in expression patterns of many duplicated genes at various evolutionary time scales and cases of gain of a new function or expression pattern by one duplicate, or partitioning of functions or expression patterns between duplicates. Alternative splicing is a fundamental aspect of the expression of many genes that can increase gene product diversity and affect gene regulation. However the evolution of alternative splicing patterns of genes duplicated by polyploidy, as well as in a sizable number of duplicated gene pairs in plants, has not been examined. Here we have characterized conservation and divergence in alternative splicing patterns in genes duplicated by a polyploidy event during the evolutionary history of Arabidopsis thaliana. We used RT-PCR to assay 104 whole genome duplicates in six organ types and in plants grown under three abiotic stress treatments to detect organ- and stress-specific patterns of alternative splicing. Differences in splicing patterns in one or more organs, or under stress conditions, were found between the genes in a large majority of the duplicated pairs. In a few cases, alternative splicing patterns were the same between duplicates only under one or more abiotic stress treatments and not under normal growing conditions, or vice versa. We also examined alternative splicing in 42 tandem duplicates and we found patterns of alternative splicing roughly comparable to the genes duplicated by polyploidy. The alternatively spliced forms in some of the genes created premature stop codons that would result in missing or partial functional domains if the transcripts are translated, which could affect gene function and cause functional divergence between duplicates. Our results indicate that alternative splicing patterns have diverged considerably after gene and genome duplication during the evolutionary history of the Arabidopsis lineage, sometimes in an organ or stress-specific manner. Alternative splicing divergence between duplicated genes may have contributed to gene functional evolution and led to preservation of some duplicated genes.

post to: CiteULike

A Population Genetic Hidden Markov Model for Detecting Genomic Regions Under Selection.

Publication Date: 2010 Feb 25 PMID: 20185453
Authors: Kern, A. D. - Haussler, D.
Journal: Mol Biol Evol

Recently, Hidden Markov Models (HMMs) have been applied to numerous problems in genomics. Here, we introduce an explicit population genetics Hidden Markov Model (popGenHMM) which uses SNP frequency data to identify genomic regions which have experienced recent selection. Our popGenHMM assumes that SNP frequencies are emitted independently following diffusion approximation expectations, but that neighboring SNP frequencies are partially correlated by selective state. We give results from the training and application of our popGenHMM to a set of early release data from the Drosophila Population Genomics Project (dpgp.org) which consists of approximately 7.8 Mb of resequencing from 32 North American Drosophila melanogaster lines. These results demonstrate the potential utility of our model, making predictions based on the site frequency spectrum for regions of the genome which represent selected elements.

post to: CiteULike

Expansion of the miRNA pathway in the hemipteran insect Acyrthosiphon pisum.

Publication Date: 2010 Feb 23 PMID: 20179251
Authors: Jaubert-Possamai, S. - Rispe, C. - Tanguy, S. - Gordon, K. - Walsh, T. - Edwards, O. - Tagu, D.
Journal: Mol Biol Evol

The pathways that allow short non-coding RNAs such as the microRNAs (miRNAs) to mediate gene regulation and control critical cellular and developmental processes involve a limited number of key protein components. These proteins are the Dicer-like RNases, double-stranded RNA-binding proteins, and the Argonaute (Ago) proteins that process stem-loop hairpin transcripts of endogenous genes to generate miRNAs, or long double-stranded RNA precursors (either exogenous or endogenous). Comparative genomics studies of metazoans have shown the pathways to be highly conserved overall; the major difference observed is that the vertebrate pathways overlap in sharing a single Dicer and Ago, while those of insects appear to be parallel, with distinct Dicers and Agos required for each pathway. The genome of the pea aphid is the first available for a hemipteran insect, and discloses an unexpected expansion of the miRNA pathway. It has two copies of the miRNA-specific Dicer-1 and Argonaute-1 genes, and four copies of Pasha, a cofactor of Drosha involved in miRNA biosynthesis. For three of these expansions, we showed that one copy of the genes diverged rapidly and in one case (Ago1b) shows signs of positive selection. These expansions occurred concomitantly within a brief evolutionary period. The pea aphid, which reproduces by viviparous parthenogenesis, is able to produce several adapted phenotypes from one single genotype. We show by RT-PCR that all the duplicated copies of the miRNA machinery genes are expressed in the different morphs. Investigating the function of these novel genes offers an exciting new challenge in aphid biology.

post to: CiteULike

Evolutionary dynamics of the Wnt gene family: a lophotrochozoan perspective.

Publication Date: 2010 Feb 22 PMID: 20176615
Authors: Cho, S. J. - Valles, Y. - Giani, V. C. Jr - Seaver, E. C. - Weisblat, D. A.
Journal: Mol Biol Evol

The Wnt gene family encodes a set of secreted glycoproteins involved in key developmental processes, including cell fate specification and regulation of posterior growth (Cadigan and Nusse 1997; Martin and Kimelman 2009). As for many other gene families, evidence for expansion and/or contraction of the wnt family is available from deuterostomes [e.g. echinoderms and vertebrates (Nusse and Varmus 1992; Schubert et al. 2000; Croce et al. 2006)] and ecdysozoans [e.g. arthropods and nematodes (Eisenmann 2005; Bolognesi et al. 2008)], but little is known from the third major bilaterian group, the lophotrochozoans [e.g. mollusks and annelids (Prud'homme et al. 2002)]. To obtain a more comprehensive scenario of the evolutionary dynamics of this gene family, we exhaustively mined wnt gene sequences from the whole genome assemblies of a mollusk (Lottia gigantea) and two annelids (Capitella teleta and Helobdella robusta), and examined them by phylogenetic, genetic linkage, intron-exon structure and embryonic expression analyses. The 36 wnt genes obtained represent 11, 12 and 9 distinct wnt subfamilies in Lottia, Capitella and Helobdella respectively. Thus, two of the three analyzed lophotrochozoan genomes retained an almost complete ancestral complement of wnt genes emphasizing the importance and complexity of this gene family across metazoans. The genome of the leech Helobdella reflects significantly more dynamism than those of Lottia and Capitella, as judged by gene duplications and losses, branch length and changes in genetic linkage. Finally, we performed a detailed expression analysis for all the Helobdella wnt genes during embryonic development. We find that, although the patterns show substantial overlap during early cleavage stages, each wnt gene has a unique expression pattern in the germinal plate and during tissue morphogenesis. Comparisons of the embryonic expression patterns of the duplicated wnt genes in Helobdella with their orthologs in Capitella reveal extensive regulatory diversification of the duplicated leech wnt genes.

post to: CiteULike

Splicing and Transcription Differ Between Spore and Intracellular Life Stages in the Parasitic Microsporidia.

Publication Date: 2010 Feb 18 PMID: 20167610
Authors: Gill, E. E. - Lee, R. C. - Corradi, N. - Grisdale, C. J. - Limpright, V. O. - Keeling, P. J. - Fast, N. M.
Journal: Mol Biol Evol

Microsporidia are a diverse group of highly-derived fungal relatives that are intracellular parasites of many animals. Both transcription and introns have been shown to be unusual in microsporidia: the complete genome of the human parasite Encephalitozoon cuniculi has only a few very short introns, and two distantly related microsporidian spores have been shown to harbour transcripts encoding several genes that overlap on different strands. However, microsporidia alternate between two life stages: the intracellular proliferative stage and the extracellular and largely metabolically dormant infectious spore. To date, most studies have focused on the spore. Here we have compared transcription profiles for a number of genes from both life stages of microsporidia, and found major differences in both the prevalence of overlapping transcription and splicing. Specifically, spore transcripts in E. cuniculi have longer 5' untranslated regions, overlap more frequently with upstream genes and have a significantly higher number of transcription initiation sites compared to intracellular transcripts from the same species. In addition, we demonstrate that splicing occurs exclusively in the intracellular stage, and not in spore mRNAs in both E. cuniculi and the distantly related Antonospora locustae. These differences between the microsporidian life stages raise questions about the functional importance of transcripts in the spore. We hypothesize that at least some transcripts in spores are a product of the cell's transition into a dormant state and that these unusual mRNAs could play a structural role rather than an informational one.

post to: CiteULike

Revisiting the insect mitochondrial molecular clock: the mid-Aegean trench calibration.

Publication Date: 2010 Feb 18 PMID: 20167609
Authors: Papadopoulou, A. - Anastasiou, I. - Vogler, A. P.
Journal: Mol Biol Evol

Phylogenetic trees in insects are frequently dated by applying a 'standard' mtDNA clock estimated at 2.3% My(-1), but despite its wide use reliable calibration points have been lacking. Here, we used a well-established biogeographic barrier, the mid-Aegean trench separating the Western and Eastern Aegean archipelago, to estimate substitution rates in tenebrionid beetles. Cytochrome Oxidase I (cox1) for six co-distributed genera across 28 islands (444 individuals) on both sides of the mid-Aegean trench revealed 60 independently coalescing entities delimited with a mixed Yule-coalescent model. One representative per entity was used for phylogenetic analysis of mitochondrial (Cytochrome Oxidase I, 16S rRNA) and nuclear (Mp20, 28SrRNA) genes. Six nodes marked geographically congruent East-West splits whose separation was largely contemporaneous and likely to reflect the formation of the mid-Aegean trench at 9-12 Mya. Based on these 'known' dates, a divergence rate of 3.54% My(-1) for the Cytochrome Oxidase I gene (2.69% when combined with the 16S rRNA gene) was obtained under the preferred partitioning scheme and substitution model selected using Bayes factors. An extensive survey suggests that discrepancies in mtDNA substitution rates in the entomological literature can be attributed to the use of different substitution models, the use of different mitochondrial gene regions, mixing of intra- with inter-specific data and not accounting for variance in coalescent times or post-separation gene flow. Different treatments of these factors in the literature confound estimates of mtDNA substitution rates in opposing directions and obscure lineage-specific differences in rates when comparing data from various sources.

post to: CiteULike

Statistical potentials for improved structurally constrained evolutionary models.

Publication Date: 2010 Feb 16 PMID: 20159780
Authors: Kleinman, C. L. - Rodrigue, N. - Lartillot, N. - Philippe, H.
Journal: Mol Biol Evol

Assessing the influence of three dimensional protein structure on sequence evolution is a difficult task, mainly because of the assumption of independence between sites required by probabilistic phylogenetic methods. Recently, models that include an explicit treatment of protein structure and site interdependencies have been developed: a statistical potential (an energy-like scoring system for sequence-structure compatibility) is used to evaluate the probability of fixation of a given mutation, assuming a coarse grain protein structure that is constant through evolution. Yet, due to the novelty of these models and the small degree of overlap between the fields of structural and evolutionary biology, only simple representations of protein structure have been used so far. In this work, we present new forms of statistical potentials, using a probabilistic framework recently developed for evolutionary studies. Terms related to pairwise distance interactions, torsion angles, solvent accessibility and flexibility of the residues are included in the potentials, so as to study the effects of the main factors known to influence protein structure. The new potentials, with a more detailed representation of the protein structure, yield a better fit than the previously used scoring functions, with pairwise interactions contributing to more than half of this improvement. In a phylogenetic context, however, the structurally constrained models are still outperformed by some of the available site-independent models in terms of fit, possibly indicating that alternatives to coarse-grained statistical potentials should be explored in order to better model structural constraints.

post to: CiteULike

Atypical subunit composition of the chlorophycean mitochondrial F1FO ATP synthase and role of Asa7 protein in stability and oligomycin resistance of the enzyme.

Publication Date: 2010 Feb 15 PMID: 20156838
Authors: Marie, L. - Adelma, E. R. - Herve, D. - Denis, B. - Elizabeth, R. S. - Nadine, C. - Marc, B. - Diego, G. H. - Claire, R. - Pierre, C.
Journal: Mol Biol Evol

Background. In yeast, mammals, and land plants, mitochondrial F(1)F(O) ATP synthase (complex V) is a remarkable enzymatic machinery which comprises about 15 conserved subunits. Peculiar among eukaryotes, complex V from Chlamydomonadales algae (order of chlorophycean class) has an atypical subunit composition of its peripheral stator and dimerization module, with 9 subunits of unknown evolutionary origin (Asa subunits). In vitro, this enzyme exhibits an increased stability of its dimeric form, and in vivo, Chlamydomonas reinhardtii cells are insensitive to oligomycins, which are potent inhibitors of proton translocation through the F(O) moiety. Methodology/Principal Findings. In this work, we showed that the atypical features of the Chlamydomonadales complex V enzyme are shared by the other chlorophycean orders. By biochemical and in silico analyses, we detected several atypical Asa subunits in Scenedesmus obliquus (Sphaeropleales) and Chlorococcum ellipsoideum (Chlorococcales). In contrast, Complex V has a canonical subunit composition in other classes of Chlorophytes (Trebouxiophyceae, Prasinophyceae, and Ulvophyceae) as well as in Streptophytes (land plants) and in Rhodophytes (red algae). Growth, respiration and ATP levels in Chlorophyceae were also barely affected by oligomycin concentrations that affect representatives of the other classes of Chlorophytes. We finally studied the function of the Asa7 atypical subunit by using RNA interference in C. reinhardtii. Although the loss of Asa7 subunit has no impact on cell bioenergetics or mitochondrial structures, it destabilizes in vitro the enzyme dimeric form and renders growth, respiration and ATP level sensitive to oligomycins. Conclusions/Significance. Altogether, our results suggest that the loss of canonical components of the Complex V stator happened at the root of chlorophycean lineage and was accompanied by the recruitment of novel polypeptides. Such a massive modification of Complex V stator features might have conferred novel properties, including the stabilization of the enzyme dimeric form and the shielding of the proton channel. In these respects, we discuss an evolutionary scenario for F(1)F(O) ATP synthase in the whole green lineage (i.e. Chlorophyta and Streptophyta).

post to: CiteULike

First-Order Correct Bootstrap Support Adjustments for Splits That Allow Hypothesis Testing When Using Maximum Likelihood Estimation.

Publication Date: 2010 Feb 12 PMID: 20154180
Authors: Susko, E.
Journal: Mol Biol Evol

The most frequent measure of phylogenetic uncertainty for splits is bootstrap support. While large bootstrap support intuitively suggests that a split in a tree is well supported it has not been clear how large bootstrap support needs to be to conclude there is significant evidence that a hypothesized split is present. Indeed, recent work has shown that bootstrap support is not first-order correct and thus cannot be directly used for hypothesis testing. We present methods that adjust bootstrap support values in a maximum likelihood setting so that they have an interpretation corresponding to p-values in conventional hypothesis testing; for instance, adjusted bootstrap support larger than 95% occurs only 5% of the time if the split is not present. Through examples and simulation settings it is found that adjustments always increase the level of support. We also find that the nature of the adjustment is fairly constant across parameter settings. Finally, we consider adjustments that take into account the data-dependent nature of many hypotheses about splits: the hypothesis that they are present is being tested because they are in the tree estimated through maximum likelihood. Here, in contrast, we find that BP often needs be adjusted downwards.

post to: CiteULike

On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila.

Publication Date: 2010 Feb 11 PMID: 20150340
Authors: Parsch, J. - Novozhilov, S. - Saminadin-Peter, S. S. - Wong, K. M. - Andolfatto, P.
Journal: Mol Biol Evol

The detection of selection, both positive and negative, acting on a DNA sequence or class of nucleotide sites requires comparison to a reference sequence that is unaffected by selection. In Drosophila, recent findings of widespread selective constraint, as well as adaptive evolution, in both coding and noncoding regions highlight the difficulties in choosing such a reference sequence. Here we investigate the utility of short intron sequences as a reference for the detection of selection. For a set of 119 D. melanogaster genes containing 195 short introns (
post to: CiteULike

Sociality is linked to rates of protein evolution in a highly social insect.

Publication Date: 2010 Mar PMID: 20110264
Authors: Hunt, B. G. - Wyder, S. - Elango, N. - Werren, J. H. - Zdobnov, E. M. - Yi, S. V. - Goodisman, M. A.
Journal: Mol Biol Evol

Eusocial insects exhibit unparalleled levels of cooperation and dominate terrestrial ecosystems. The success of eusocial insects stems from the presence of specialized castes that undertake distinct tasks. We investigated whether the evolutionary transition to societies with discrete castes was associated with changes in protein evolution. We predicted that proteins with caste-biased gene expression would evolve rapidly due to reduced antagonistic pleiotropy. We found that queen-biased proteins of the honeybee Apis mellifera did indeed evolve rapidly, as predicted. However, worker-biased proteins exhibited slower evolutionary rates than queen-biased or nonbiased proteins. We suggest that distinct selective pressures operating on caste-biased genes, rather than a general reduction in pleiotropy, explain the observed differences in evolutionary rates. Our study highlights, for the first time, the interaction between highly social behavior and dynamics of protein evolution.

post to: CiteULike

Evidence for multiple independent origins of trans-splicing in Metazoa.

Publication Date: 2010 Mar PMID: 19942614
Authors: Douris, V. - Telford, M. J. - Averof, M.
Journal: Mol Biol Evol

In contrast to conventional splicing, which joins exons from a single primary transcript, trans-splicing links stretches of RNA from separate transcripts, derived from distinct regions of the genome. Spliced leader (SL) trans-splicing is particularly well known in trypanosomes, nematodes, and flatworms, where it provides messenger RNAs with a leader sequence and cap that allow them to be translated efficiently. One of the largest puzzles regarding SL trans-splicing is its evolutionary origin. Until now SL trans-splicing has been found in a small and disparate set of organisms (including trypanosomes, dinoflagellates, cnidarians, rotifers, nematodes, flatworms, and urochordates) but not in most other eukaryotic lineages, including well-studied groups such as fungi, plants, arthropods, and vertebrates. This patchy distribution could either suggest that trans-splicing was present in early eukaryotes/metazoans and subsequently lost in multiple lineages or that it evolved several times independently. Starting from the serendipitous discovery of SL trans-splicing in an arthropod, we undertook a comprehensive survey of this process in the animal kingdom. By surveying expressed sequence tag data from more than 70 metazoan species, we show that SL trans-splicing also occurs in at least two groups of arthropods (amphipod and copepod crustaceans), in ctenophores, and in hexactinellid sponges. However, we find no evidence for SL trans-splicing in other groups of arthropods and sponges or in 15 other phyla that we have surveyed. Although the presence of SL trans-splicing in hydrozoan cnidarians, hexactinellid sponges, and ctenophores might suggest that it was present at the base of the Metazoa, the patchy distribution that is evident at higher resolution suggests that SL trans-splicing has evolved repeatedly among metazoan lineages. In agreement with this scenario, we discuss evidence that SL precursor RNAs can readily evolve from ubiquitous small nuclear RNAs that are used for conventional splicing.

post to: CiteULike

Polymorphic competence peptides do not restrict recombination in Streptococcus pneumoniae.

Publication Date: 2010 Mar PMID: 19942613
Authors: Cornejo, O. E. - McGee, L. - Rozen, D. E.
Journal: Mol Biol Evol

Understanding the factors that limit recombination in bacteria is critical in order to better understand and assess its effects on genetic variation and bacterial population genetic structure. Transformation in the naturally competent bacterium, Streptococcus pneumoniae, is regulated by a polymorphic competence (com) apparatus. It has been suggested that polymorphic types, called pherotypes, generate and maintain subpopulation genetic structure within this species. We test predictions stemming from this hypothesis using a cosmopolitan sample of clinical pneumococcal isolates. We sequenced the locus encoding the peptide that induces competence (comC) to assign clones to each known pherotype class and then used multilocus sequence typing to determine whether there is significant genetic differentiation between pherotypes subgroups. We find two dominant pherotypes within our sample, and both are maintained at high frequencies (CSP1 74%, CSP2 26%). Our analyses fail to detect significant genetic differentiation between pherotype groups and find strong evidence, from a coalescent analysis, for interpherotype recombination. In addition, our analyses indicate that positive selection may account for the maintenance of the fixed polymorphism in this locus (comC). Altogether, these results fail to support the prediction that the polymorphism in the competence system acts to limit recombination within S. pneumoniae populations. We discuss why this result is expected given the mechanism underlying transformation and outline a scenario to explain the evolution of polymorphism in the competence system.

post to: CiteULike

Comparative gene evolution in haemosporidian (apicomplexa) parasites of birds and mammals.

Publication Date: 2010 Mar PMID: 19933837
Authors: Outlaw, D. C. - Ricklefs, R. E.
Journal: Mol Biol Evol

Haemosporidian parasites of birds and mammals reproduce asexually inside nucleated and nonnucleated host erythrocytes, respectively. Because of these different parasite environments and because bird parasites are paraphyletic, we evaluated whether patterns of parasite molecular evolution differ between host groups. We compared two mitochondrial (mt) genes and one apicoplast gene across mammal Plasmodium, bird Plasmodium, and bird Parahaemoproteus. Using a molecular phylogenetic approach, we show that the parasite mt cytochrome b (cyt b), mt cytochrome oxidase I (COI), and the apicoplast caseinolytic protease C (ClpC) exhibit similar levels of sequence divergence, yet each gene tree presents a strikingly different pattern of internal versus terminal branch lengths. In cyt b, the ratio of nonsynonymous (NS)-to-synonymous substitutions (d(N)/d(S)) is markedly elevated along the internal branch linking mammalian and avian parasites despite the sister relationship between mammal and bird Plasmodium. This is not the case for either COI or ClpC. When NS substitutions are excluded from the parasite cyt b alignment, the resulting phylogenetic tree resembles that of COI (both with and without NS substitutions). The high d(N)/d(S) ratio in the cyt b branch separating avian and mammalian parasites and a mammal-parasite codon bias suggest that adaptive evolution has distinguished mammal and bird parasites.

post to: CiteULike

Evolution of an X-linked primate-specific micro RNA cluster.

Publication Date: 2010 Mar PMID: 19933172
Authors: Li, J. - Liu, Y. - Dong, D. - Zhang, Z.
Journal: Mol Biol Evol

Micro RNAs (miRNAs) are a class of small regulatory RNAs, which posttranscriptionally repress protein production of the targeted messenger RNAs (mRNAs). Accumulating evidence has suggested lineage-specific miRNAs have contributed to lineage-specific characteristics. However, the birth and death of these miRNAs, particularly in primates, largely remain unexplored. We herein characterized the evolutionary history of a newly discovered miRNA cluster on primate X-chromosome, spanning a approximately 33-kb region in human Xq27.3. The cluster consists of six distinct miRNAs, four of which are compactly organized in a 3-kb region belonging to a phylogenetic group distinct from the other two miRNAs. By comparing the genomic structure of this cluster in human with four other primates (chimpanzee, orangutan, rhesus macaque, and marmoset), we identified several previously uncovered miRNAs in these primates that share orthology with the human miRNAs. We found the entire miRNA cluster was well conserved among primate species but unidentifiable in other mammalian species (including mouse, rat, cat, dog, horse, cow, opossum, and platypus), suggesting that the formation of this cluster was after the primate-rodent split but before the emergence of New-World Monkey (represented by marmoset). Our analysis further revealed complex evolutionary dynamics on this locus, characterized by extensive duplication events. Phylogenetic analysis revealed birth and death of the miRNAs within this region, accompanied by rapid evolution, which highlighted their functional importance. These miRNAs are primarily expressed in primate epididymis, part of the male reproductive system. Our analysis showed that their predicted target mRNAs are significantly enriched for several functional classes relevant to epididymal physiology, such as morphogenesis of epithelium and tube development. Furthermore, several genes controlling sperm maturation and male fertility are confidently predicted to be their targets. Collectively, we argue these miRNAs might play an important role in epididymal morphogenesis and sperm maturation and in establishing primate-specific epididymal characteristics.

post to: CiteULike

Faster-Z evolution is predominantly due to genetic drift.

Publication Date: 2010 Mar PMID: 19926635
Authors: Mank, J. E. - Nam, K. - Ellegren, H.
Journal: Mol Biol Evol

Genes linked to sex chromosomes may show different levels of functional change than autosomal genes due to different evolutionary pressures. We used whole-genome data from zebra finch-chicken orthologs to test for Faster-Z evolution, finding that Z-linked genes evolve up to 50% more rapidly than autosomal genes. We combined these divergence data with information about sex-specific expression patterns in order to determine whether the Faster-Z Effect that we observe was predominantly the result of positive selection of recessive beneficial mutations in the heterogametic sex or primarily due to genetic drift attributable to the lower effective population size of the Z chromosome compared with an autosome. The Faster-Z Effect was no more prevalent for genes expressed predominantly in females; therefore, our data indicate that the largest source of Faster-Z Evolution is the increased levels of genetic drift on the Z chromosome. This is likely a product of sexual selection acting on males, which reduces the effective population size of the Z relative to that of the autosomes. Additionally, this latter result suggests that the relative evolutionary pressures underlying Faster-Z Evolution are different from those in analogous Faster-X Evolution.

post to: CiteULike

Comparing models of evolution for ordered and disordered proteins.

Publication Date: 2010 Mar PMID: 19923193
Authors: Brown, C. J. - Johnson, A. K. - Daughdrill, G. W.
Journal: Mol Biol Evol

Most models of protein evolution are based upon proteins that form relatively rigid 3D structures. A significant fraction of proteins, the so-called disordered proteins, do not form rigid 3D structures and sample a broad conformational ensemble. Disordered proteins do not typically maintain long-range interactions, so the constraints on their evolution should be different than ordered proteins. To test this hypothesis, we developed and compared models of evolution for disordered and ordered proteins. Substitution matrices were constructed using the sequences of putative homologs for sets of experimentally characterized disordered and ordered proteins. Separate matrices, at three levels of sequence similarity (>85%, 85-60%, and 60-40%), were inferred for each type of protein structure. The substitution matrices for disordered and ordered proteins differed significantly at each level of sequence similarity. The disordered matrices reflected a greater likelihood of evolutionary changes, relative to the ordered matrices, and these changes involved nonconservative substitutions. Glutamic acid and asparagine were interesting exceptions to this result. Important differences between the substitutions that are accepted in disordered proteins relative to ordered proteins were also identified. In general, disordered proteins have fewer evolutionary constraints than ordered proteins. However, some residues like tryptophan and tyrosine are highly conserved in disordered proteins. This is due to their important role in forming protein-protein interfaces. Finally, the amino acid frequencies for disordered proteins, computed during the development of the matrices, were compared with amino acid frequencies for different categories of secondary structure in ordered proteins. The highest correlations were observed between the amino acid frequencies in disordered proteins and the solvent-exposed loops and turns of ordered proteins, supporting an emerging structural model for disordered proteins.

post to: CiteULike

Molecular evolution in bacterial endosymbionts of fungi.

Publication Date: 2010 Mar PMID: 19923192
Authors: Castillo, D. M. - Pawlowska, T. E.
Journal: Mol Biol Evol

The prediction that progressive coupling of host and symbiont metabolic and reproductive interests leads to reduced mixing of symbiont lineages has been verified extensively in maternally transmitted bacterial endosymbionts of insects. To test whether this prediction is also applicable to associations of bacteria with fungi, we explored patterns of molecular evolution in two lineages of mutualistic endosymbionts of fungi: the Burkholderia endosymbionts of Rhizopus microsporus (Mucormycotina) and Candidatus Glomeribacter gigasporarum endosymbionts of arbuscular mycorrhizal fungi (Glomeromycota). We compared these two lineages with the closely related Candidatus Tremblaya princeps endosymbionts of mealybugs (Hemiptera, Coccoidea, Pseudococcidae) and to free-living Burkholderia species. To make inferences about the life histories of the endosymbionts, we relied on the empirically validated predictions of the nearly neutral theory of molecular evolution that a reduction of the effective population size increases the rate of fixation of slightly deleterious mutations. Our analyses showed that the slightly deleterious mutation accumulation patterns in the Burkholderia endosymbionts of Rhizopus were nearly indistinguishable from those in their free-living relatives. In contrast, Ca. Glomeribacter showed unique patterns of molecular evolution that differentiated them from both the Burkholderia endosymbionts of Rhizopus and from the Ca. Tremblaya endosymbionts of insects. These findings imply that reduced mixing of symbiont lineages is not a universal feature of symbioses between fungi and endocellular bacteria.

post to: CiteULike

Parallel evolution of nacre building gene sets in molluscs.

Publication Date: 2010 Mar PMID: 19915030
Authors: Jackson, D. J. - McDougall, C. - Woodcroft, B. - Moase, P. - Rose, R. A. - Kube, M. - Reinhardt, R. - Rokhsar, D. S. - Montagnani, C. - Joubert, C. - Piquemal, D. - Degnan, B. M.
Journal: Mol Biol Evol

The capacity to biomineralize is closely linked to the rapid expansion of animal life during the early Cambrian, with many skeletonized phyla first appearing in the fossil record at this time. The appearance of disparate molluscan forms during this period leaves open the possibility that shells evolved independently and in parallel in at least some groups. To test this proposition and gain insight into the evolution of structural genes that contribute to shell fabrication, we compared genes expressed in nacre (mother-of-pearl) forming cells in the mantle of the bivalve Pinctada maxima and the gastropod Haliotis asinina. Despite both species having highly lustrous nacre, we find extensive differences in these expressed gene sets. Following the removal of housekeeping genes, less than 10% of all gene clusters are shared between these molluscs, with some being conserved biomineralization genes that are also found in deuterostomes. These differences extend to secreted proteins that may localize to the organic shell matrix, with less than 15% of this secretome being shared. Despite these differences, H. asinina and P. maxima both secrete proteins with repetitive low-complexity domains (RLCDs). Pinctada maxima RLCD proteins-for example, the shematrins-are predominated by silk/fibroin-like domains, which are absent from the H. asinina data set. Comparisons of shematrin genes across three species of Pinctada indicate that this gene family has undergone extensive divergent evolution within pearl oysters. We also detect fundamental bivalve-gastropod differences in extracellular matrix proteins involved in mollusc-shell formation. Pinctada maxima expresses a chitin synthase at high levels and several chitin deacetylation genes, whereas only one protein involved in chitin interactions is present in the H. asinina data set, suggesting that the organic matrix on which calcification proceeds differs fundamentally between these species. Large-scale differences in genes expressed in nacre-forming cells of Pinctada and Haliotis are compatible with the hypothesis that gastropod and bivalve nacre is the result of convergent evolution. The expression of novel biomineralizing RLCD proteins in each of these two molluscs and, interestingly, sea urchins suggests that the evolution of such structural proteins has occurred independently multiple times in the Metazoa.

post to: CiteULike

Eukaryotic and eubacterial contributions to the establishment of plastid proteome estimated by large-scale phylogenetic analyses.

Publication Date: 2010 Mar PMID: 19910386
Authors: Suzuki, K. - Miyagishima, S. Y.
Journal: Mol Biol Evol

Plastids including chloroplasts arose from a cyanobacterial endosymbiont and have retained their own genome, but the size has been reduced to less than one-tenth of the original bacterial genome. Over time, genes essential to plastid function have been transferred from the ancestral plastid genome to the nucleus, and the gene products are now targeted into the plastid from the host cytosol. However, phylogenetic analyses have suggested that the functions of certain original proteins encoded by the endosymbiont genome have been replaced by nucleus-encoded proteins of noncyanobacterial origin and that several proteins have been newly added to maintain and control plastids. In order to evaluate the rate and origin of noncyanobacterial proteins that have contributed to the establishment of the plastid proteome, we performed phylogenetic analyses of plastid-targeted proteins that are shared by the red alga Cyanidioschyzon merolae (455 proteins) and the Viridiplanta Arabidopsis thaliana (744 proteins). Our results show that approximately 40% of the plastid proteome common to red algae and green plants originated from genes of both the ancestral eukaryotic host and various lineages of bacteria (eubacteria) other than cyanobacteria. The replacement or addition of components was frequently observed for most of the plastid functions except for the light reaction of photosynthesis and the translation and degradation of proteins in the plastid. These results suggest that a considerable amount of bacterial metagenomic material, as well as the genomes of the host and the endosymbiont, has contributed to the establishment of the plastid before the split of the red and green algae.

post to: CiteULike

Highly expressed and slowly evolving proteins share compositional properties with thermophilic proteins.

Publication Date: 2010 Mar PMID: 19910385
Authors: Cherry, J. L.
Journal: Mol Biol Evol

The sequences of proteins encoded by a genome evolve at different rates. A correlate of a protein's evolutionary rate is its expression level: highly expressed proteins tend to evolve slowly. Some explanations of rate variation and the correlation between rate and expression predict that more slowly evolving and more highly expressed proteins have more favorable equilibrium constants for folding. Proteins from thermophiles generally have more stable folds than proteins from mesophiles, and it is known that there are systematic differences in amino acid content between thermophilic and mesophilic proteins. I examined whether there are analogous correlations of amino acid frequencies with evolutionary rate and expression level within genomes. In most of the organisms analyzed, there is a striking tendency for more slowly evolving proteins to be more thermophile-like in their amino acid compositions when adjustments are made for variation in GC content. More highly expressed proteins also tend to be more thermophile-like by the same criteria. These results suggest that part of the evolutionary rate variation among proteins is due to variation in the strength of selection for stability of the folded state. They also suggest that increasing strength of this selective force with expression level plays a role in the correlation between evolutionary rate and expression level.

post to: CiteULike

Lateral phage transfer in obligate intracellular bacteria (wolbachia): verification from natural populations.

Publication Date: 2010 Mar PMID: 19906794
Authors: Chafee, M. E. - Funk, D. J. - Harrison, R. G. - Bordenstein, S. R.
Journal: Mol Biol Evol

Lateral transfer of mobile DNA is a hallmark of bacteria with a free-living replicative stage; however, its significance in obligate intracellular bacteria and other heritable endosymbionts remains controversial. Comparative sequence analyses from laboratory stocks infected with Wolbachia pipientis provide some of the most compelling evidence that bacteriophage WO-B transfers laterally between infections of the same insect host. Lateral transfer between coinfections, however, has been evaluated neither in natural populations nor between closely related Wolbachia strains. Here, we analyze bacterial and phage genes from two pairs of natural sympatric field isolates, of Gryllus pennsylvanicus field crickets and of Neochlamisus bebbianae leaf beetles, to demonstrate WO-B transfers between supergroup B Wolbachia. N. bebbianae revealed the highest number of phage haplotypes yet recorded, hinting that lab lines could underestimate phage haplotype variation and lateral transfer. Finally, using the approximate age of insect host species as the maximum available time for phage transfer between host-associated bacteria, we very conservatively estimate phage WO-B transfer to occur at least once every 0-5.4 My within a host species. Increasing discoveries of mobile elements, intragenic recombination, and bacterial coinfections in host-switching obligate intracellular bacteria specify that mobile element transfer is common in these species.

post to: CiteULike

Bayesian inference of species trees from multilocus data.

Publication Date: 2010 Mar PMID: 19906793
Authors: Heled, J. - Drummond, A. J.
Journal: Mol Biol Evol

Until recently, it has been common practice for a phylogenetic analysis to use a single gene sequence from a single individual organism as a proxy for an entire species. With technological advances, it is now becoming more common to collect data sets containing multiple gene loci and multiple individuals per species. These data sets often reveal the need to directly model intraspecies polymorphism and incomplete lineage sorting in phylogenetic estimation procedures. For a single species, coalescent theory is widely used in contemporary population genetics to model intraspecific gene trees. Here, we present a Bayesian Markov chain Monte Carlo method for the multispecies coalescent. Our method coestimates multiple gene trees embedded in a shared species tree along with the effective population size of both extant and ancestral species. The inference is made possible by multilocus data from multiple individuals per species. Using a multiindividual data set and a series of simulations of rapid species radiations, we demonstrate the efficacy of our new method. These simulations give some insight into the behavior of the method as a function of sampled individuals, sampled loci, and sequence length. Finally, we compare our new method to both an existing method (BEST 2.2) with similar goals and the supermatrix (concatenation) method. We demonstrate that both BEST and our method have much better estimation accuracy for species tree topology than concatenation, and our method outperforms BEST in divergence time and population size estimation.

post to: CiteULike

Compensatory molecular evolution of HC-Pro, an RNA-silencing suppressor from a plant RNA virus.

Publication Date: 2010 Mar PMID: 19906792
Authors: Torres-Barcelo, C. - Daros, J. A. - Elena, S. F.
Journal: Mol Biol Evol

RNA silencing is a eukaryotic mechanism involved in several cellular processes, one example being a sequence-specific antiviral defense. Many plant viruses have developed counterdefensive proteins that in many instances are multifunctional, such as helper component protease (HC-Pro) of Tobacco etch virus (TEV). In a previous work, a collection of mutants with amino acid replacements in TEV HC-Pro was generated, and their effects in the capacity of suppressing RNA silencing were quantified in a transient expression assay. In this study, three mutations that caused a reduction in suppression activity and three that increased it were used to create replicate experimental lineages that were evolved through serial passages. We have evaluated the number of genotypic changes that occurred during evolution in HC-Pro and their phenotypic effects on virus viability, virulence, and suppression of RNA silencing. In no instance did the original mutation revert to the wildtype (WT) sequence. In several cases, fixed mutations were canonical compensatory changes, returning the suppressor activity to the WT HC-Pro value, pointing to the existence of stabilizing selection pressures and pleiotropic effects of the introduced original mutations. However, in other instances, the fixed mutations were overcompensatory, driving the activity of the mutant beyond the optimal value. Negative epistatic effects among beneficial mutations as well as decompensatory epistasis also play an important role during compensatory evolution of RNA-silencing suppression.

post to: CiteULike

Evolutionary fingerprinting of genes.

Publication Date: 2010 Mar PMID: 19864470
Authors: Pond, S. L. - Scheffler, K. - Gravenor, M. B. - Poon, A. F. - Frost, S. D.
Journal: Mol Biol Evol

Over time, natural selection molds every gene into a unique mosaic of sites evolving rapidly or resisting change-an "evolutionary fingerprint" of the gene. Aspects of this evolutionary fingerprint, such as the site-specific ratio of nonsynonymous to synonymous substitution rates (dN/dS), are commonly used to identify genetic features of potential biological interest; however, no framework exists for comparing evolutionary fingerprints between genes. We hypothesize that protein-coding genes with similar protein structure and/or function tend to have similar evolutionary fingerprints and that comparing evolutionary fingerprints can be useful for discovering similarities between genes in a way that is analogous to, but independent of, discovery of similarity via sequence-based comparison tools such as Blast. To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates.

post to: CiteULike

Vertebrate rhodopsin adaptation to dim light via rapid meta-II intermediate formation.

Publication Date: 2010 Mar PMID: 19858068
Authors: Sugawara, T. - Imai, H. - Nikaido, M. - Imamoto, Y. - Okada, N.
Journal: Mol Biol Evol

Rhodopsin is a photoreceptive protein present in vertebrate rod photoreceptor cells, which are responsible for scotopic vision. Recent molecular studies have shown that several aquatic vertebrate species have independently acquired rhodopsin containing Asp83Asn, Glu122Gln, and Ala292Ser substitutions, causing a blue shift in the rhodopsin absorption spectra for adaptation to the blue-green photic environment in deep water. Here, we provide new evidence for the evolutionary and functional relevance of the Asp83Asn substitution. Spectroscopic and kinetic analyses of rhodopsins in six cichlid fishes from the East African Great Lakes using charge-coupled device spectrophotometer revealed that the Asp83Asn substitution accelerated the formation of meta-II, a rhodopsin intermediate crucial for activation of the G-protein transducin. Because rapid formation of meta-II likely results in effective transduction of photic signals, it is reasonable to assume that deep-water cichlid species have acquired rhodopsin containing Asn83 to adapt to dim lighting. Remarkably, rhodopsin containing Asn83 has been identified in terrestrial vertebrates such as bats, and these rhodopsin variants also exhibit accelerated meta-II formation. Our results indicated that the Asp83Asn substitution observed in a variety of animal species was acquired independently in many different lineages during vertebrate evolution for adaptation to dimly lit environments.

post to: CiteULike

Evidence that localized variation in primate sequence divergence arises from an influence of nucleosome placement on DNA repair.

Publication Date: 2010 Mar PMID: 19843619
Authors: Ying, H. - Epps, J. - Williams, R. - Huttley, G.
Journal: Mol Biol Evol

Understanding the origins of localized substitution rate heterogeneity has important implications for identifying functional genomic sequences. Outside of gene regions, the origins of rate heterogeneity remain unclear. Experimental studies establish that chromatin compaction affects rates of both DNA lesion formation and repair. A functional association between chromatin status and 5-methyl-cytosine also exists. These suggest that both the total rate and the type of substitution will be affected by chromatin status. Regular positioning of nucleosomes, the building block of chromatin, further predicts that substitution rate and type should vary spatially in an oscillating manner. We addressed chromatin's influence on substitution rate and type in primates. Matched numbers of sites were sampled from Dnase I hypersensitive (DHS) and closed chromatin control flank (Flank). Likelihood ratio tests revealed significant excesses of total and of transition substitutions in Flank compared with matched DHS for both intergenic and intronic samples. An additional excess of CpG transitions was evident for the intergenic, but not intronic, regions. Fluctuation in substitution rate along approximately 1,800 primate promoters was measured using phylogenetic footprinting. Significant positive correlations were evident between the substitution rate and a nucleosome score from resting human T-cells, with up to approximately 50% of the variance in substitution rate accounted for. Using signal processing techniques, a dominant oscillation at approximately 200 bp was evident in both the substitution rate and the nucleosome score. Our results support a role for differential DNA repair rates between open and closed chromatin in the spatial distribution of rate heterogeneity.

post to: CiteULike

Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula.

Publication Date: 2010 Mar PMID: 19837657
Authors: Ingvarsson, P. K.
Journal: Mol Biol Evol

One important goal of population genetics is to understand the relative importance of different evolutionary processes for shaping variation in natural populations. Here, I use multilocus data to show that natural selection on both synonymous and nonsynonymous mutations plays an important role in shaping levels of synonymous polymorphism in European aspen (Populus tremula). Previous studies have documented a preferential fixation of synonymous mutations encoding preferred codons in P. tremula. The results presented here show that this has resulted in an increase in codon bias in P. tremula, consistent with stronger selection acting on synonymous codon usage. In addition, positive selection on nonsynonymous mutations appears to be common in P. tremula, with approximately 30% of all mutations having been fixed by positive selection. In addition, the recurrent fixation of beneficial mutations also reduces standing levels of polymorphism as evidenced by a significantly negative relationship between the rate of protein evolution synonymous site diversity and silent site diversity. Finally, I use approximate Bayesian methods to estimate the strength of selection acting on beneficial substitutions. These calculations show that recurrent hitchhiking reduces polymorphism by, on average, 30%. The product of strength of selection acting on beneficial mutations and the rate by which these occur across the genome (2N(e)lambdas) equals 1.54x10( - 7), which is in line with estimates from Drosophila where recurrent hitchhiking has also been shown to have significant effects on standing levels of polymorphism.

post to: CiteULike

Fast and consistent estimation of species trees using supermatrix rooted triples.

Publication Date: 2010 Mar PMID: 19833741
Authors: DeGiorgio, M. - Degnan, J. H.
Journal: Mol Biol Evol

Concatenated sequence alignments are often used to infer species-level relationships. Previous studies have shown that analysis of concatenated data using maximum likelihood (ML) can produce misleading results when loci have differing gene tree topologies due to incomplete lineage sorting. Here, we develop a polynomial time method that utilizes the modified mincut supertree algorithm to construct an estimated species tree from inferred rooted triples of concatenated alignments. We term this method SuperMatrix Rooted Triple (SMRT) and use the notation SMRT-ML when rooted triples are inferred by ML. We use simulations to investigate the performance of SMRT-ML under Jukes-Cantor and general time-reversible substitution models for four- and five-taxon species trees and also apply the method to an empirical data set of yeast genes. We find that SMRT-ML converges to the correct species tree in many cases in which ML on the full concatenated data set fails to do so. SMRT-ML can be conservative in that its output tree is often partially unresolved for problematic clades. We show analytically that when the species tree is clocklike and mutations occur under the Cavender-Farris-Neyman substitution model, as the number of genes increases, SMRT-ML is increasingly likely to infer the correct species tree even when the most likely gene tree does not match the species tree. SMRT-ML is therefore a computationally efficient and statistically consistent estimator of the species tree when gene trees are distributed according to the multispecies coalescent model.

post to: CiteULike

Estimates of the effect of natural selection on protein-coding content.

Publication Date: 2010 Mar PMID: 19815689
Authors: Yap, V. B. - Lindsay, H. - Easteal, S. - Huttley, G.
Journal: Mol Biol Evol

Analysis of natural selection is key to understanding many core biological processes, including the emergence of competition, cooperation, and complexity, and has important applications in the targeted development of vaccines. Selection is hard to observe directly but can be inferred from molecular sequence variation. For protein-coding nucleotide sequences, the ratio of nonsynonymous to synonymous substitutions (omega) distinguishes neutrally evolving sequences (omega = 1) from those subjected to purifying (omega < 1) or positive Darwinian (omega > 1) selection. We show that current models used to estimate omega are substantially biased by naturally occurring sequence compositions. We present a novel model that weights substitutions by conditional nucleotide frequencies and which escapes these artifacts. Applying it to the genomes of pathogens causing malaria, leprosy, tuberculosis, and Lyme disease gave significant discrepancies in estimates with approximately 10-30% of genes affected. Our work has substantial implications for how vaccine targets are chosen and for studying the molecular basis of adaptive evolution.

post to: CiteULike

Footprints of X-to-Y gene conversion in recent human evolution.

Publication Date: 2010 Mar PMID: 19812029
Authors: Trombetta, B. - Cruciani, F. - Underhill, P. A. - Sellitto, D. - Scozzari, R.
Journal: Mol Biol Evol

Different X-homologous regions of the male-specific portion of the human Y chromosome (MSY) are characterized by a different content of putative single nucleotide polymorphisms (SNPs), as reported in public databases. The possible role of X-to-Y nonallelic gene conversion in contributing to these differences remains poorly understood. We explored this issue by analyzing sequence variation in three regions of the MSY characterized by a different degree of X-Y similarity and a different density of putative SNPs: the PCDH11Y gene in the X-transposed (X-Y identity 99%, high putative SNP content); the TBL1Y gene in the X-degenerate (X-Y identity 86-88%, low putative SNP content); and VCY genes-containing region in the P8 palindrome (X-Y identity 95%, low putative SNP content). Present findings do not provide any evidence for gene conversion in the PCDH11Y and TBL1Y genes; they also strongly suggest that most putative SNPs of the PCDH11Y gene (and possibly the entire X-transposed region) are most likely X-Y paralogous sequence variants, which have been entered in the databases as SNPs. On the other hand, clear evidence for the VCY genes in the P8 palindrome having acted as an acceptor of X-to-Y gene conversion was obtained. A rate of 1.8 x 10(-7) X-to-Y conversions/bp/year was estimated for these genes. These findings indicate that in the VCY region of the MSY, X-to-Y gene conversion can be highly effective to increase the level of diversity among human Y chromosomes and suggest an additional explanation for the ability of the Y chromosome to retard degradation during evolution. Present data are expected to pave the way for future investigations on the role of nonallelic gene conversion in double-strand break repair and the maintenance of Y chromosome integrity.

post to: CiteULike

Inference and characterization of horizontally transferred gene families using stochastic mapping.

Publication Date: 2010 Mar PMID: 19808865
Authors: Cohen, O. - Pupko, T.
Journal: Mol Biol Evol

Macrogenomic events, in which genes are gained and lost, play a pivotal evolutionary role in microbial evolution. Nevertheless, probabilistic-evolutionary models describing such events and methods for their robust inference are considerably less developed than existing methodologies for analyzing site-specific sequence evolution. Here, we present a novel method for the inference of gains and losses of gene families. First, we develop probabilistic-evolutionary models describing the dynamics of gene-family content, which are more biologically realistic than previously suggested models. In our likelihood-based models, gains and losses are represented by transitions between presence and absence, given an underlying phylogeny. We employ a mixture-model approach in which we allow both the gain rate and the loss rate to vary among gene families. Second, we use these models together with the analytic implementation of stochastic mapping to infer branch-specific events. Our novel methodology allows us to infer and quantify horizontal gene transfer (HGT) events. This enables us to rank various gene families and lineages according to their propensity to undergo gains and losses. Applying our methodology to 4,873 gene families shows that: 1) the novel mixture models describe the observed variability in gene-family content among microbes significantly better than previous models; 2) The stochastic mapping approach enables accurate inference of gain and loss events based on simulations; 3) At least 34% of the gene families analyzed are inferred to have experienced HGT at least once during their evolution; and 4) Gene families that were inferred to experience HGT are both enriched and depleted with respect to specific functional categories.

post to: CiteULike