Molecular Biology and Evolution

Effects of X-linkage and sex-biased gene expression on the rate of adaptive protein evolution in Drosophila.

Publication Date: 2008 May 13 PMID: 18477586
Authors: Baines, J. F. - Sawyer, S. A. - Hartl, D. L. - Parsch, J.
Journal: Mol Biol Evol

Patterns of polymorphism and divergence in Drosophila protein-coding genes suggest that a considerable fraction of amino acid differences between species can be attributed to positive selection and that genes with sex-biased expression, i.e. those expressed predominantly in one sex, have especially high rates of adaptive evolution. Previous studies, however, have been restricted to autosomal sex-biased genes and, thus, do not provide a complete picture of the evolutionary forces acting on sex-biased genes across the genome. To determine the effects of X-linkage on sex-biased gene evolution, we surveyed DNA sequence polymorphism and divergence in 45 X-linked genes, including 17 with male-biased expression, 13 with female-biased expression, and 15 with equal expression in the two sexes. Using both single- and multi-locus tests for selection, we found evidence for adaptive evolution in both groups of sex-biased genes. The signal of adaptive evolution was particularly strong for X-linked male-biased genes. A comparison with data from 91 autosomal genes revealed a "fast-X" effect, in which the rate of adaptive evolution was greater for X-linked than for autosomal genes. This effect was strongest for male-biased genes, but could be seen in the other groups as well. A genome-wide analysis of coding sequence divergence that accounted for sex-biased expression also uncovered a fast-X effect for male-biased and unbiased genes, suggesting that recessive beneficial mutations play an important role in adaptation.

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The guanine nucleotide exchange factors Sec2 and PRONE: candidate synapomorphies for the Opisthokonta and the Archaeplastida.

Publication Date: 2008 May 13 PMID: 18477585
Authors: Elias, M.
Journal: Mol Biol Evol

Although recent multi-gene phylogenetic analyses support close relationship of Metazoa and Fungi (the eukaryotic supergroup Opisthokonta) and monophyly of eukaryotes with the primary plastid, i.e. Chloroplastida, Rhodophyta, and Glaucophyta (the supergroup Archaeplastida or Plantae), some authors still challenge this scheme. I found that two particular types of guanine nucleotide exchange factors (GEFs, i.e., cofactors of GTPases) might provide a new piece of evidence to resolve this controversy. An exhaustive analysis of available sequence data revealed that Sec2-related proteins, known to serve as GEF for exocytic GTPases of the Rab8/Sec4 subfamily, are restricted to opisthokonts, whereas proteins with the PRONE domain, recently described as novel plant-specific GEFs for RHO family GTPases, occur only in Chloroplastida and Rhodophyta. The results thus point to possible evolutionary innovations in the exocytic apparatus of the ancestral opisthokonts and reveal the probably first plastid-independent trait (i.e., a unique mode of RHO GTPase regulation) exclusive for Chloroplastida+Rhodophyta, further supporting monophyly of these two groups.

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Mitochondrial DNA phylogeny in Eastern and Western Slavs.

Publication Date: 2008 May 13 PMID: 18477584
Authors: Malyarchuk, B. - Grzybowski, T. - Derenko, M. - Perkova, M. - Vanecek, T. - Lazur, J. - Gomolcak, P. - Tsybovsky, I.
Journal: Mol Biol Evol

To resolve the phylogeny of certain mitochondrial DNA (mtDNA) haplogroups in Eastern Europe and estimate their evolutionary age, a total of 73 samples representing mitochondrial haplogroups U4, HV*, and R1 were selected for complete mitochondrial genome sequencing from a collection of about 2000 control-region sequences sampled in Eastern (Russians, Belorussians, Ukrainians) and Western (Poles, Czechs and Slovaks) Slavs. On the basis of whole-genome resolution, we fully characterized a number of haplogroups (HV3, HV4, U4a1, U4a2, U4a3, U4b, U4c, U4d, and R1a) that were previously described only partially. Our findings demonstrate that haplogroups HV3, HV4, and U4a1 could be traced back to the pre-Neolithic times ( approximately 12,000-19,000 YBP) in Eastern Europe. In addition, an ancient connection between the Caucasus/Europe and India has been revealed by analysis of haplogroup R1 diversity, with a split between the Indian and Caucasus/European R1a lineages occurring about 16,500 years ago. Meanwhile, some mtDNA subgroups detected in Slavs (such as U4a2a, U4a2*, HV3a, R1a1) are definitely younger being dated between 6,400-8,200 YBP. However, robust age estimations appear to be problematic due to the high ratios of non-synonymous to synonymous substitutions found in young mtDNA subclusters.

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Convergent evolution of clustering of Iroquois homeobox genes across metazoans.

Publication Date: 2008 May 9 PMID: 18469332
Authors: Irimia, M. - Maeso, I. - Garcia-Fernandez, J.
Journal: Mol Biol Evol

Vertebrate and Drosophila Iroquois genes are organized in clusters of three genes sharing blocks of conserved regulatory sequences. Here, we report a three-gene cluster in the basal, pre-duplicative chordate amphioxus. Surprisingly, however, the origin of the amphioxus cluster is independent of those in vertebrates and drosophilids. Investigation of genomic organization of Iroquois genes in other 17 metazoan genomes revealed a fourth independent three-gene cluster organization in polychaetes, as well as additional two- and four-gene clusters in other clades, in one of the most striking examples of convergence in genomic organization described so far. The recurrent independent evolution of Iroquois clusters suggests a functional importance of this organization for these genes, perhaps related to the sharing of regulatory elements. Consistent with this, comparative analysis of genomic regions flanking the three amphioxus Irx genes revealed several blocks of sequences, conserved for at least 100 million years. Finally, we discuss the possible causes and implications of the convergent evolution of this genomic and regulatory organization throughout metazoans.

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DNA METHYLATION AND STRUCTURAL AND FUNCTIONAL BIMODALITY OF VERTEBRATE PROMOTERS.

Publication Date: 2008 May 9 PMID: 18469331
Authors: Elango, N. - Yi, S. V.
Journal: Mol Biol Evol

Human promoters divide into two classes, the low CpG (LCG) and the high CpG (HCG), based on their CpG dinucleotide content. The LCG class of promoters is hyper-methylated and is associated with tissue-specific genes, while the HCG class is hypo-methylated and associated with broadly-expressed genes. By analyzing several chordate genomes separated for hundreds of millions of years, here we show that the divide between low CpG and high CpG promoters is conserved in several distantly related vertebrate taxa (including human, chicken, frog, lizard, and fish), but not in close invertebrate outgroups (sea squirts). Furthermore, LCG and HCG promoters are distinctively associated with tissue-specific and broadly expressed genes in these distantly related vertebrate taxa. Our results indicate that the function of DNA methylation on gene expression is conserved across these vertebrate taxa and suggest that the two classes of promoters have evolved early in vertebrate evolution, as a consequence of the advent of global DNA methylation.

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The deep archaeal roots of eukaryotes.

Publication Date: 2008 May 6 PMID: 18463089
Authors: Yutin, N. - Makarova, K. S. - Mekhedov, S. L. - Wolf, Y. I. - Koonin, E. V.
Journal: Mol Biol Evol

The set of conserved eukaryotic protein-coding genes includes distinct subsets one of which appears to be most closely related to and, by inference, derived from archaea, whereas another one appears to be of bacterial, possibly, endosymbiotic origin. The "archaeal" genes of eukaryotes, primarily, encode components of information-processing systems whereas the "bacterial" genes are predominantly operational. The precise nature of the archaeo-eukaryotic relationship remains uncertain, and it has been variously argued that eukaryotic informational genes evolved from the homologous genes of Euryarchaeota or Crenarchaeota (the major branches of extant archaea), or that the origin of eukaryotes lies outside the known diversity of archaea. We describe a comprehensive set of 355 eukaryotic genes of apparent archaeal origin identified through ortholog detection and phylogenetic analysis. Phylogenetic hypothesis testing using constrained trees, combined with a systematic search for shared derived characters in the form of homologous inserts in conserved proteins, indicate that, for the majority of these genes, the preferred tree topology is one with the eukaryotic branch placed outside the extant diversity of archaea although small subsets of genes show crenarchaeal and euryarchaeal affinities. Thus, the "archaeal" genes in eukaryotes appear to descend from a distinct, ancient, and otherwise uncharacterized archaeal lineage that acquired some euryarchaeal and crenarchaeal genes via early horizontal gene transfer.

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Long-Term Balancing Selection at the West-Nile Virus Resistance Gene, Oas1b, Maintains Trans-Specific Polymorphisms in the House Mouse.

Publication Date: 2008 May 5 PMID: 18460447
Authors: Ferguson, W. - Dvora, S. - Gallo, J. - Orth, A. - Boissinot, S.
Journal: Mol Biol Evol

Oligo-Adenylate Synthetases (OAS) are interferon-inducible enzymes that participate in the first line of defense against a wide range of viral infection. Recent studies have determined that Oas1b, a member of the OAS gene family in the house mouse (Mus musculus), provides specific protection against flavivirus infection (e.g. West Nile virus, Dengue Fever virus and Yellow Fever virus). We characterized the nucleotide sequence variation in coding and non-coding regions of the Oas1b gene for a large number of wild-derived strains of M. musculus, and related species. Our sequence analyses determined that this gene is one of the most polymorphic genes ever described in any mammal. The level of variation in non-coding regions of Oas1b is an order of magnitude higher than the level reported for other regions of the mouse genome and is significantly different from the level of intra-specific variation expected under neutrality. Furthermore, a phylogenetic analysis of intronic sequences demonstrated that Oas1b alleles are ancient and that their divergence pre-dates several speciation events, resulting in trans-specific polymorphisms. The amino-acid sequence of Oas1b is also extremely variable, with 1 out of 7 amino-acid positions being polymorphic within M. musculus. Oas1b alleles are comparatively more divergent at synonymous positions than most autosomal genes and the ratio of non-synonymous to synonymous substitution is remarkably high, suggesting that positive selection has been acting on Oas1b. The ancestry of Oas1b polymorphisms and the high level of amino-acid polymorphisms strongly suggest that the allelic variation at Oas1b has been maintained in mouse populations by long-term balancing selection.

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Distinct evolutionary patterns between chemoreceptors of two vertebrate olfactory systems and the differential tuning hypothesis.

Publication Date: 2008 May 5 PMID: 18460446
Authors: Grus, W. E. - Zhang, J.
Journal: Mol Biol Evol

Most tetrapod vertebrates have two olfactory systems, the main olfactory system (MOS) and the vomeronasal system (VNS). According to the dual olfactory hypothesis, the MOS detects environmental odorants while the VNS recognizes intraspecific pheromonal cues. However, this strict functional distinction has been blurred by recent reports that both systems can perceive both types of signals. Studies of a limited number of receptors suggest that MOS receptors are broadly tuned generalists while VNS receptors are narrowly tuned specialists. However, whether this distinction applies to all MOS and VNS receptors remains unknown. The differential tuning hypothesis predicts that generalist MOS receptors detect an overlapping set of ligands and thus are more likely to be conserved over evolutionary time than specialist VNS receptors, which would evolve in a more lineage-specific manner. Here we test this prediction for all olfactory chemoreceptors by examining the evolutionary patterns of MOS-expressed odorant receptors (ORs) and trace amine associated receptors (TAARs) and VNS-expressed vomeronasal type 1 receptors (V1Rs) and type 2 receptors (V2Rs) in seven tetrapods (mouse, rat, dog, opossum, platypus, chicken, and frog). The phylogenies of V1Rs and V2Rs show abundant lineage-specific gene gains/losses and virtually no one-to-one orthologs between species. Opposite patterns are found for ORs and TAARs. Analysis of functional data and ligand-binding sites of ORs confirms that paralogous chemoreceptors are more likely than orthologs to have different ligands and that functional divergence between paralogous chemoreceptors is established relatively quickly following gene duplication. Together, these results strongly suggest that the functional profile of the VNS chemoreceptor repertoire evolves much faster than that of the MOS chemoreceptor repertoire and that the differential tuning hypothesis applies to the majority, if not all, of MOS and VNS receptors.

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How well does the HoT score reflect sequence alignment accuracy?

Publication Date: 2008 May 4 PMID: 18458029
Authors: Hall, B. G.
Journal: Mol Biol Evol

Multiple sequence alignment is an essential tool in many areas of biological research, and the accuracy of an alignment can strongly affect the accuracy of a downstream application such as phylogenetic analysis, identification of functional motifs or PCR primer design. The HoT (Heads or Tails) method (Landan and Graur 2007) assesses the consistency of an alignment by comparing the alignment of a set of sequences with the alignment of the same set of sequences written in reverse order. This study shows that HoT scores and the alignment accuracies are positively correlated, so alignments with higher HoT scores are preferable. However, HoT scores are overestimates of alignment accuracy in general, with the extent of overestimation depending on the method used for multiple sequence alignment.

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Substitution of the gene for chloroplast RPS16 was assisted by generation of a dual targeting signal.

Publication Date: 2008 May 2 PMID: 18453549
Authors: Ueda, M. - Nishikawa, T. - Fujimoto, M. - Takanashi, H. - Arimura, S. I. - Tsutsumi, N. - Kadowaki, K. I.
Journal: Mol Biol Evol

Organelle (mitochondria and chloroplasts in plants) genomes lost a large number of genes after endosymbiosis occurred. Even after this major gene loss, organelle genomes still lose their own genes, even those that are essential, via gene transfer to the nucleus and gene substitution of either different organelle origin or de novo genes. Gene transfer and substitution events are important processes in the evolution of the eukaryotic cell. Gene loss is an ongoing process in the mitochondria and chloroplasts of higher plants. The gene for ribosomal protein S16 (rps16) is encoded in the chloroplast genome of most higher plants, but not in Medicago truncatula and Populus alba. Here, we show that these two species have compensated for loss of the rps16 from the chloroplast genome by having a mitochondrial rps16 that can target the chloroplasts as well as mitochondria. Furthermore, in Arabidopsis thaliana, Lycopersicon esculentum, and Oryza sativa, whose chloroplast genomes encode the rps16, we show that the product of the mitochondrial rps16 has dual targeting ability. These results suggest that the dual targeting of RPS16 to the mitochondria and chloroplasts emerged before the divergence of monocots and dicots (140-150 Myr ago). The gene substitution of the chloroplast rps16 by the nuclear-encoded rps16 in higher plants is the first report about ongoing gene substitution by dual targeting and provides evidence for an intermediate stage in the formation of this heterogeneous organelle.

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Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Datasets.

Publication Date: 2008 May 2 PMID: 18453548
Authors: Prasad, A. B. - Allard, M. W. - Green, E. D.
Journal: Mol Biol Evol

The ongoing generation of prodigious amounts of genomic sequence data from myriad vertebrates is providing unparalleled opportunities for establishing definitive phylogenetic relationships among species. The size and complexities of such comparative sequence datasets allow smaller and more-difficult branches to be resolved, but also present unique challenges, including large computational requirements and the negative consequences of systematic biases. To explore these issues and to clarify the phylogenetic relationships among mammals, we have analyzed a large dataset of over 60 megabase pairs (Mb) of high-quality genomic sequence, which we generated from 41 mammals and 3 other vertebrates. All sequences are orthologous to a 1.9-Mb region of the human genome that encompasses the cystic fibrosis transmembrane conductance regulator gene (CFTR). To understand the characteristics and challenges associated with phylogenetic analyses of such a large dataset, we partitioned the sequence data in several ways, and utilized maximum likelihood, maximum parsimony, and neighbor joining algorithms, implemented in parallel on Linux clusters. These studies yielded well-supported phylogenetic trees, largely confirming other recent molecular phylogenetic analyses. Our results provide support for rooting the placental mammal tree between Atlantogenata (Xenarthra and Afrotheria) and Boreoeutheria (Euarchontoglires and Laurasiatheria), illustrate the difficulty in resolving some branches even with large amounts of data (e.g., in the case of Laurasiatheria), and demonstrate the valuable role that very large comparative sequence datasets can play in refining our understanding of the evolutionary relationships of vertebrates.

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Duplication and functional diversification of HAP3 genes leading to the origin of the seed-developmental regulatory gene, LEAFY COTYLEDON1 (LEC1), in non-seed plant genomes.

Publication Date: 2008 May 2 PMID: 18453547
Authors: Xie, Z. - Li, X. - Glover, B. J. - Bai, S. - Rao, G. Y. - Luo, J. - Yang, J.
Journal: Mol Biol Evol

The HAP3 gene encodes a subunit of the CCAAT-box binding factor (CBF), a highly conserved trimeric activator that recognizes and binds the ubiquitous CCAAT promoter element with high affinity. Two types of HAP3 gene have been identified in plant genomes. The LEC1-type HAP3 genes encode a functionally specialized subunit of CBF, which is expressed specifically in developing seeds. In contrast, most non-LEC1-type HAP3 genes are expressed in various tissues. It has been proposed that the LEC1-type HAP3genes originated from the duplication and functional divergence of non-LEC1-type HAP3 genes. However, it is not yet known when this duplication event took place or whether the LEC1-type HAP3genes appeared at the same time as the origin of seed plants. Here we describe a comprehensive comparison of the duplication patterns of HAP3 genes in different plant genomes. We recognize a major expansion of the HAP3 gene family accompanying the origin and early diversification of land plants, and postulate that retrotransposition and other mechanisms of gene duplication have been involved in the expansion of the plant HAP3 gene family. We provide evidence that the LEC1-type HAP3genes originated in non-seed vascular plant genomes, and demonstrate that they are inductively expressed under drought stress in non-seed plants. These genes, however, were recruited to a novel regulatory network in the early stages of seed plant evolution and steadily expressed during seed development and maturation.

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Co-expression of Linked Genes in Mammalian Genomes is Generally Disadvantageous.

Publication Date: 2008 Apr 24 PMID: 18440951
Authors: Liao, B. Y. - Zhang, J.
Journal: Mol Biol Evol

Similarity in gene expression pattern between closely linked genes is known in several eukaryotes. Two models have been proposed to explain the presence of such co-expression patterns. The adaptive model assumes that co-expression is advantageous and is established by relocation of initially unlinked but co-expressed genes, whereas the neutral model asserts that co-expression is a type of leaky expression due to similar expressional environments of linked genes, but is neither advantageous nor detrimental. However, these models are incompatible with several empirical observations. Here, we propose that co-expression of linked genes is a form of transcriptional interference that is disadvantageous to the organism. We show that even distantly linked genes that are tens of megabases away exhibit significant co-expression in the human genome. However, the linkage is more likely to be broken during evolution between genes of high co-expression than those of low co-expression and the breakage of linkage reduces gene co-expression. These results support our hypothesis that co-expression of linked genes in mammalian genomes is generally disadvantageous, implying that many mammalian genes may never reach their optimal expression pattern due to the interference of their genomic environment and that such transcriptional interference may be a force promoting recurrent relocation of genes in the genome.

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Influence of the mutant spectrum in viral evolution: focused selection of antigenic variants in a reconstructed viral quasispecies.

Publication Date: 2008 Apr 23 PMID: 18436553
Authors: Martin, V. - Domingo, E.
Journal: Mol Biol Evol

RNA viruses replicate as complex mutant distributions termed viral quasispecies. Despite this, studies on virus populations subjected to positive selection have generally been performed and analyzed as if the viral population consisted of a defined genomic nucleotide sequence; such a simplification may not reflect accurately the molecular events underlying the selection process. In the present study we have reconstructed a foot-and-mouth disease virus quasispecies with multiple, low frequency, genetically distinguishable mutants that can escape neutralization by a monoclonal antibody. Some of the mutants included an amino acid substitution that affected an integrin-recognition motif that overlaps with the antibody-binding site, while other mutants included an amino acid substitution that affected antibody binding but not integrin recognition. We have monitored consensus and clonal nucleotide sequences of populations passaged either in the absence or the presence of the neutralizing antibody. In both cases, the populations focused towards a specific mutant that was surrounded by a cloud of mutants with different antigenic and cell recognition specificities. In the absence of antibody selection, an antigenic variant that maintained integrin recognition became dominant, but the mutant cloud included as one of its minority components a variant with altered integrin recognition. Conversely, in the presence of antibody selection, a variant with altered integrin-recognition motif became dominant, but it was surrounded by a cloud of antigenic variants that maintained integrin recognition. The results have documented that a mutant spectrum can exert an influence on a viral population subjected to a sustained positive selection pressure, and have unveiled a mechanism of antigenic flexibility in viral populations, consisting in the presence in the selected quasispecies of mutants with different antigenic and cell recognition specificities.

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Genetic exchange vs genetic differentiation in a medium-sized inversion of Drosophila: the A2/Ast arrangements of D. subobscura.

Publication Date: 2008 Apr 23 PMID: 18436552
Authors: Nobrega, C. - Kahdem, M. - Aguade, M. - Segarra, C.
Journal: Mol Biol Evol

Chromosomal inversion polymorphism affects nucleotide variation at loci associated with inversions. In D. subobscura, a species with a rich chromosomal inversion polymorphism and the largest recombinational map so far reported in the Drosophila genus, extensive genetic structure of nucleotide variation was detected in the segment affected by the O(3) inversion, a moderately-sized inversion at Muller's element E. Indeed, a strong genetic differentiation all over O(3) and no evidence of a higher genetic exchange in the center of the inversion than at breakpoints were detected. In order to ascertain, whether other polymorphic and differently sized inversions of D. subobscura also exhibited a strong genetic structure, nucleotide variation in five gene regions (P236, P275, P150, Sxl and P125) located along the A(2) inversion was analyzed in A(st) and A(2) chromosomes of D. subobscura. A(2) is a medium-sized inversion at Muller's element A and forms a single inversion loop in heterokaryotypes. The lower level of variation in A(2) relative to A(st) and the significant excess of low frequency variants at polymorphic sites indicate that nucleotide variation at A(2) is not at mutation-drift equilibrium. The closest region to an inversion breakpoint, P236, exhibits the highest level of genetic differentiation (F(ST)) and of linkage disequilibrium between arrangements and variants at nucleotide polymorphic sites (LD). The remaining four regions show a higher level of genetic exchange between A(2) and A(st) chromosomes than P236, as revealed by F(ST) and LD estimates. However, significant genetic differentiation between the A(st) and A(2) arrangements was detected not only at P236, but also in the other four regions separated from the nearest breakpoint by 1.2 Mb to 2.9 Mb. Therefore, the extent of genetic exchange between arrangements has not been high enough to homogenize nucleotide variation in the center of the A(2) inversion. A(2) can be considered a typical successful inversion of D. subobscura according to its relative length. Chromosomal inversion polymorphism of D. subobscura might thus cause the genome of this species to be highly structured and to harbor different gene pools that might contribute to maintain adaptations to particular environments.

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Differential Evolution of the Thirteen Atlantic Salmon Hox Clusters.

Publication Date: 2008 Apr 18 PMID: 18424774
Authors: Mungpakdee, S. - Seo, H. C. - Angotzi, A. R. - Dong, X. - Akalin, A. - Chourrout, D.
Journal: Mol Biol Evol

Hox cluster organization represents a valuable marker to study the effects of recent genome duplication in salmonid fish (25-100 million years ago). Using PCR amplification of cDNAs, BAC library screening and genome walking, we reconstructed 13 Hox clusters in the Atlantic salmon containing 118 Hox genes including 8 pseudogenes. Hox paralogs resulting from the genome duplication preceding the radiation of ray-finned fish have been much better preserved in salmon than in other model teleosts. The last genome duplication in the salmon lineage has been followed by the loss of one of the four HoxA clusters. Four rounds of genome duplication after the vertebrate ancestor, salmon Hox clusters display the main organizational features of vertebrate Hox clusters, with Hox genes exclusively that are densely packed in the same orientation. Recently duplicated Hox clusters have engaged a process of divergence, with several cases of pseudogenization or asymmetrical evolution of Hox gene duplicates, and a marked erosion of identity in non-coding sequences. Strikingly, the level of divergence attained strongly depends on the Hox cluster pairs, rather than on the Hox genes within each cluster. It is particularly high between both HoxBb clusters and both HoxDa clusters, while both HoxBa clusters remained virtually identical. Positive selection on the Hox protein coding sequences could not be detected.

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Difficulties in Testing for Covarion-Like Properties of Sequences Under the Confounding Influence of Changing Proportions of Variable Sites.

Publication Date: 2008 Apr 18 PMID: 18424773
Authors: Gruenheit, N. - Lockhart, P. J. - Steel, M. - Martin, W.
Journal: Mol Biol Evol

The covarion-like properties of sequences are poorly described and their impact on phylogenetic analyses poorly understood. We demonstrate using simulations that, under an evolutionary model where the proportion of variable sites changes in non adjacent lineages, log likelihood values for rates across site (RAS) and covarion (COV) models become similar, making models difficult to distinguish. Further, although COV and RAS models provide a great improvement in likelihood scores over a homogeneous model with these simulated data, reconstruction accuracy of tree building is low, suggesting caution when it is suspected that proportions of variable sites differ in different evolutionary lineages. We study the performance of a recently developed contingency test that detects the presence of COV-type evolution modified for protein data. We report that if proportions of variable sites (p(var)) change in a lineage-specific manner such that their distributions in different lineages become sufficiently non-overlapping, then the contingency test can incorrectly suggest a homogeneous model. Also of concern is the possibility of different proportions of variable sites between the groups being studied. In a study of chloroplast proteins, interpretation of the test is found to be susceptible to different partitioning of taxon groups, making the test very subjective in its implementation. Extreme intergroup differences in the extent of divergence and difference in proportions of variable sites could be contributing to this effect.

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Bayesian Inference of Errors in Ancient DNA Caused by Post Mortem Degradation.

Publication Date: 2008 Apr 16 PMID: 18420593
Authors: Mateiu, L. M. - Rannala, B.
Journal: Mol Biol Evol

Methods for extracting and amplifying sequences using ancient DNA (aDNA) can be prone to errors caused by post mortem modifications of the DNA strand. A new statistical method is developed for predicting errors in aDNA sequences caused by such processes. In addition to the canonical DNA substitution model parameters, a discrete Markov chain is used to describe nucleotide substitutions occurring via post mortem degradation of the aDNA sequences. A computer program, BYPASSR-degr, was developed implementing the method and was used in subsequent analyses of simulated datasets under the new model. Simulation studies show that the new method can be powerful and accurate in identifying damaged sites. The method is applied to analyze aDNA sequences of Etruscans, Adelie penguins and horses. No significant signals of degradation were observed at any sites of the aDNA sequences we analyzed.

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Molecular Cloning and Characterization of a Moss (Ceratodon purpureus) Non-Symbiotic Hemoglobin Provides Insight into the Early Evolution of Plant Non-Symbiotic Hemoglobins.

Publication Date: 2008 Apr 16 PMID: 18420592
Authors: Garrocho-Villegas, V. - Arredondo-Peter, R.
Journal: Mol Biol Evol

Non-symbiotic hemoglobins (nsHbs) are widespread in plants, including bryophytes. Bryophytes (such as mosses) are among the oldest land plants, thus an analysis of a bryophyte nsHb is of interest from an evolutionary perspective. However, very little is known about bryophyte nsHbs. Here, we report the cloning and characterization of a nshb gene (cerhb) from the moss Ceratodon purpureus. Sequence analysis showed that cerhb is interrupted by three introns in identical position as all known plant nshb genes, which suggests that the ancestral nshb gene was interrupted by three introns. Expression analysis showed that cerhb expresses in protonemas and gametophytes growing in normal conditions, and that it overexpresses in protonemas subjected to osmotic (sucrose), heat shock, cold and nitrate stress conditions. Also, modeling of the CerHb tertiary structure suggests that CerHb is hexacoordinate and that it binds O2 with high affinity. Comparative analysis of the predicted CerHb with native rice Hb1 and soybean Lba structures revealed that the major evolutionary changes that probably occurred during the evolution of plant Hbs were (i) a hexacoordinate to pentacoordinate transition at the heme prosthetic group, (ii) a length decrease at the CD-loop and N- and C-termini regions, and (iii) the compaction of the protein into a globular structure.

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Local adaptation and vector-mediated population structure in Plasmodium vivax malaria.

Publication Date: 2008 Jun PMID: 18385220
Authors: Joy, D. A. - Gonzalez-Ceron, L. - Carlton, J. M. - Gueye, A. - Fay, M. - McCutchan, T. F. - Su, X. Z.
Journal: Mol Biol Evol

Plasmodium vivax in southern Mexico exhibits different infectivities to 2 local mosquito vectors, Anopheles pseudopunctipennis and Anopheles albimanus. Previous work has tied these differences in mosquito infectivity to variation in the central repeat motif of the malaria parasite's circumsporozoite (csp) gene, but subsequent studies have questioned this view. Here we present evidence that P. vivax in southern Mexico comprised 3 genetic populations whose distributions largely mirror those of the 2 mosquito vectors. Additionally, laboratory colony feeding experiments indicate that parasite populations are most compatible with sympatric mosquito species. Our results suggest that reciprocal selection between malaria parasites and mosquito vectors has led to local adaptation of the parasite. Adaptation to local vectors may play an important role in generating population structure in Plasmodium. A better understanding of coevolutionary dynamics between sympatric mosquitoes and parasites will facilitate the identification of molecular mechanisms relevant to disease transmission in nature and provide crucial information for malaria control.

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Retrotransposition as a source of new promoters.

Publication Date: 2008 Jun PMID: 18367464
Authors: Okamura, K. - Nakai, K.
Journal: Mol Biol Evol

The fact that promoters are essential for the function of all genes presents the basis of the general idea that retrotranspositions give rise to processed pseudogenes. However, recent studies have demonstrated that some retrotransposed genes are transcriptionally active. Because promoters are not thought to be retrotransposed along with exonic sequences, these transcriptionally active genes must have acquired a functional promoter by mechanisms that are yet to be determined. Hence, comparison between a retrotransposed gene and its source gene appears to provide a unique opportunity to investigate the promoter creation for a new gene. Here, we identified 29 gene pairs in the human genome, consisting of a functional retrotransposed gene and its parental gene, and compared their respective promoters. In more than half of these cases, we unexpectedly found that a large part of the core promoter had been transcribed, reverse transcribed, and then integrated to be operative at the transposed locus. This observation can be ascribed to the recent discovery that transcription start sites tend to be interspersed rather than situated at 1 specific site. This propensity could confer retrotransposability to promoters per se. Accordingly, the retrotransposability can explain the genesis of some alternative promoters.

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Fast evolution of core promoters in primate genomes.

Publication Date: 2008 Jun PMID: 18367463
Authors: Liang, H. - Lin, Y. S. - Li, W. H.
Journal: Mol Biol Evol

Despite much interest in regulatory evolution, how promoters have evolved remains poorly studied, mainly owing to paucity of data on promoter regions. Using a new set of high-quality experimentally determined core promoters of the human genome, we conducted a comparative analysis of 2,492 human and rhesus macaque promoters and their neighboring nearly neutral regions. We found that the core promoters have an average rate of nucleotide substitution substantially higher than that at 4-fold degenerate sites and only slightly lower than that for the assumed neutral controls of neighboring noncoding regions, suggesting that core promoters are subject to very weak selective constraints. Interestingly, we identified 24 core promoters (at false discovery rate = 50%) that have evolved at an accelerated rate compared with the neutral controls, suggesting that they may have undergone positive selection. The inferred positively selected genes show strong bias in molecular function. We also used population genetic approaches to examine the evolution of core promoters in human populations and found evidence of positive selection at some loci. Taken together, our results suggest that positive selection has played a substantial role in the evolution of transcriptional regulation in primates.

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An information-theoretic method for the treatment of plural ancestry in phylogenetics.

Publication Date: 2008 Jun PMID: 18359947
Authors: Munshaw, S. - Kepler, T. B.
Journal: Mol Biol Evol

In the presence of recombination and gene conversion, a given genomic segment may inherit information from 2 distinct immediate ancestors. The importance of this type of molecular inheritance has become increasingly clear over the years, and the potential for erroneous inference when it is not accounted for in the statistical model is well documented. Yet, the inclusion of plural ancestry (PA) in phylogenetic analysis is still not routine. This omission is due to the greater difficulty of phylogenetic inference on general acyclic graphs compared that on with trees and the accompanying computational burden. We have developed a technique for phylogenetic inference in the presence of PA based on the principle of minimum description length, which assigns a cost--the description length--to each network topology given the observed sequence data. The description length combines the cost of poor data fit and model complexity in terms of information. This device allows us to search through network topologies to minimize the total description length. By comparing the best models obtained with and without PA, one can determine whether or not recombination has played an active role in the evolution of the genes under investigation, identify those genes that appear to be mosaic, and infer the phylogenetic network that best represents the history of the alignment. We show that the method performs well on simulated data and demonstrate its application on HIV env gene sequence data from 8 human subjects. The software implementation of the method is available upon request.

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Climate change and postglacial human dispersals in southeast Asia.

Publication Date: 2008 Jun PMID: 18359946
Authors: Soares, P. - Trejaut, J. A. - Loo, J. H. - Hill, C. - Mormina, M. - Lee, C. L. - Chen, Y. M. - Hudjashov, G. - Forster, P. - Macaulay, V. - Bulbeck, D. - Oppenheimer, S. - Lin, M. - Richards, M. B.
Journal: Mol Biol Evol

Modern humans have been living in Island Southeast Asia (ISEA) for at least 50,000 years. Largely because of the influence of linguistic studies, however, which have a shallow time depth, the attention of archaeologists and geneticists has usually been focused on the last 6,000 years--in particular, on a proposed Neolithic dispersal from China and Taiwan. Here we use complete mitochondrial DNA (mtDNA) genome sequencing to spotlight some earlier processes that clearly had a major role in the demographic history of the region but have hitherto been unrecognized. We show that haplogroup E, an important component of mtDNA diversity in the region, evolved in situ over the last 35,000 years and expanded dramatically throughout ISEA around the beginning of the Holocene, at the time when the ancient continent of Sundaland was being broken up into the present-day archipelago by rising sea levels. It reached Taiwan and Near Oceania more recently, within the last approximately 8,000 years. This suggests that global warming and sea-level rises at the end of the Ice Age, 15,000-7,000 years ago, were the main forces shaping modern human diversity in the region.

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Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax.

Publication Date: 2008 Jun PMID: 18359945
Authors: Roy, S. W. - Irimia, M.
Journal: Mol Biol Evol

Despite substantial work, the phylogeny of malaria parasites remains debated. The matter is complicated by concerns about patterns of evolution in potentially strongly selected genes as well as the extreme AT bias of some Plasmodium genomes. Particularly contentious has been the position of the most virulent human parasite Plasmodium falciparum, whether grouped with avian parasites or within a larger clade of mammalian parasites. Here, we study 3 classes of rare genomic changes, as well as the sequences of mitochondrial ribosomal RNA (rRNA) genes. We report 3 lines of support for a clade of mammalian parasites: 1) we find no instances of spliceosomal intron loss in a hypothetical ancestor of P. falciparum and the avian parasite Plasmodium gallinaceum, suggesting against a close relationship between those species; 2) we find 4 genomic mitochondrial indels supporting a mammalian clade, but none grouping P. falciparum with avian parasites; and 3) slowly evolving mitochondrial rRNA sequences support a mammalian parasite clade with 100% posterior probability. We further report a large deletion in the mitochondrial large subunit rRNA gene, which suggests a subclade including both African and Asian parasites within the clade of closely related primate malarias. This contrasts with previous studies that provided strong support for separate Asian and African clades, and reduces certainty about the historical and geographic origins of Plasmodium vivax. Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium.

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Alveolins, a new family of cortical proteins that define the protist infrakingdom Alveolata.

Publication Date: 2008 Jun PMID: 18359944
Authors: Gould, S. B. - Tham, W. H. - Cowman, A. F. - McFadden, G. I. - Waller, R. F.
Journal: Mol Biol Evol

Alveolates are a recently recognized group of unicellular eukaryotes that unites disparate protists including apicomplexan parasites (which cause malaria and toxoplasmosis), dinoflagellate algae (which cause red tides and are symbionts in many corals), and ciliates (which are microscopic predators and common rumen symbionts). Gene sequence trees provide robust support for the alveolate alliance, but beyond the common presence of membranous sacs (alveoli) subtending the plasma membrane, the group has no unifying morphological feature. We describe a family of proteins, alveolins, associated with these membranous sacs in apicomplexa, dinoflagellates, and ciliates. Alveolins contain numerous simple peptide repeats and are encoded by multigene families. We generated antibodies against a peptide motif common to all alveolins and identified a range of apparently abundant proteins in apicomplexa, dinoflagellates, and ciliates. Immunolocalization reveals that alveolins are associated exclusively with the cortical regions of apicomplexa, dinoflagellates, and ciliates where the alveolar sacs occur. Alveolins are the first molecular nexus between the unifying structures that defines this eukaryotic group. They provide an excellent opportunity to explore the exceptional compartment that was apparently the key to a remarkable diversification of unique protists that occupy a wide array of lifestyle niches.

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A cryptic algal group unveiled: a plastid biosynthesis pathway in the oyster parasite Perkinsus marinus.

Publication Date: 2008 Jun PMID: 18359776
Authors: Matsuzaki, M. - Kuroiwa, H. - Kuroiwa, T. - Kita, K. - Nozaki, H.
Journal: Mol Biol Evol

Plastids are widespread in plant and algal lineages. They are also exploited by some nonphotosynthetic protists, including malarial parasites, to support their diverse modes of life. However, cryptic plastids may exist in other nonphotosynthetic protists, which could be important in studies on the diversity and evolution of plastids. The parasite Perkinsus marinus, which causes mass mortality in oyster farms, is a nonphotosynthetic protist that is phylogenetically related to plastid-bearing dinoflagellates and apicomplexans. In this study, we searched for P. marinus methylerythritol phosphate (MEP) pathway genes, responsible for de novo isoprenoid synthesis in plastids, and determined the full-length gene sequences for 6 of 7 of these genes. Phylogenetic analyses revealed that each P. marinus gene clusters with orthologs from plastid-bearing eukaryotes, which have MEP pathway genes with essentially the same mosaic pattern of evolutionary origin. A new analytical method called sliding-window iteration of TargetP was developed to examine the distribution of targeting preferences. This analysis revealed that the sequenced genes encode bipartite targeting peptides that are characteristic of proteins targeted to secondary plastids originating from endosymbiosis of eukaryotic algae. These results support our idea that Perkinsus is a cryptic algal group containing nonphotosynthetic secondary plastids. In fact, immunofluorescent microscopy indicated that 1 of the MEP pathway enzymes, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, was localized to small compartments near mitochondrion, which are possibly plastids. This tiny organelle seems to contain very low quantities of DNA or may even lack DNA entirely. The MEP pathway genes are a useful tool for investigating plastid evolution in both of the photosynthetic and nonphotosynthetic eukaryotes and led us to propose the hypothesis that ancestral "chromalveolates" harbored plastids before a secondary endosymbiotic event.

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Evolutionary patterns of MHC class II B in owls and their implications for the understanding of avian MHC evolution.

Publication Date: 2008 Jun PMID: 18359775
Authors: Burri, R. - Hirzel, H. N. - Salamin, N. - Roulin, A. - Fumagalli, L.
Journal: Mol Biol Evol

Owing to its special mode of evolution and central role in the adaptive immune system, the major histocompatibility complex (MHC) has become the focus of diverse disciplines such as immunology, evolutionary ecology, and molecular evolution. MHC evolution has been studied extensively in diverse vertebrate lineages over the last few decades, and it has been suggested that birds differ from the established mammalian norm. Mammalian MHC genes evolve independently, and duplication history (i.e., orthology) can usually be traced back within lineages. In birds, this has been observed in only 3 pairs of closely related species. Here we report strong evidence for the persistence of orthology of MHC genes throughout an entire avian order. Phylogenetic reconstructions of MHC class II B genes in 14 species of owls trace back orthology over tens of thousands of years in exon 3. Moreover, exon 2 sequences from several species show closer relationships than sequences within species, resembling transspecies evolution typically observed in mammals. Thus, although previous studies suggested that long-term evolutionary dynamics of the avian MHC was characterized by high rates of concerted evolution, resulting in rapid masking of orthology, our results question the generality of this conclusion. The owl MHC thus opens new perspectives for a more comprehensive understanding of avian MHC evolution.

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Evolutionary genomics of host adaptation in vesicular stomatitis virus.

Publication Date: 2008 Jun PMID: 18353798
Authors: Remold, S. K. - Rambaut, A. - Turner, P. E.
Journal: Mol Biol Evol

Populations experiencing similar selection pressures can sometimes diverge in the genetic architectures underlying evolved complex traits. We used RNA virus populations of large size and high mutation rate to study the impact of historical environment on genome evolution, thus increasing our ability to detect repeatable patterns in the evolution of genetic architecture. Experimental vesicular stomatitis virus populations were evolved on HeLa cells, on MDCK cells, or on alternating hosts. Turner and Elena (2000. Cost of host radiation in an RNA virus. Genetics. 156:1465-1470.) previously showed that virus populations evolved in single-host environments achieved high fitness on their selected hosts but failed to increase in fitness relative to their ancestor on the unselected host and that alternating-host-evolved populations had high fitness on both hosts. Here we determined the complete consensus sequence for each evolved population after 95 generations to gauge whether the parallel phenotypic changes were associated with parallel genomic changes. We also analyzed the patterns of allele substitutions to discern whether differences in fitness across hosts arose through true pleiotropy or the presence of not only a mutation that is beneficial in both hosts but also 1 or more mutations at other loci that are costly in the unselected environment (mutation accumulation [MA]). We found that ecological history may influence to what extent pleiotropy and MA contribute to fitness asymmetries across environments. We discuss the degree to which current genetic architecture is expected to constrain future evolution of complex traits, such as host use by RNA viruses.

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The cbb3 oxidases are an ancient innovation of the domain bacteria.

Publication Date: 2008 Jun PMID: 18353797
Authors: Ducluzeau, A. L. - Ouchane, S. - Nitschke, W.
Journal: Mol Biol Evol

A survey of genomes for the presence of gene clusters related to cbb(3) oxidases detected bona fide members of the family in almost all phyla of the domain Bacteria. No archaeal representatives were found. The subunit composition was seen to vary substantially between clades observed on the phylogenetic tree of the catalytic subunit CcoN. The protein diade formed by CcoN and the monoheme cytochrome CcoO appears to constitute the functionally essential "core" of the enzyme conserved in all sampled cbb(3) gene clusters. The topology of the phylogenetic tree contradicts the scenario of a recent origin of cbb(3) oxidases and substantiates the status of this family as a phylogenetic entity on the same level as the other subgroups of the heme-copper superfamily (including nitric oxide reductase). This finding resuscitates and exacerbates the conundrum of the evolutionary origin of heme-copper oxidases.

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Emergence of polyproline II-like structure at early stages of experimental evolution from random polypeptides.

Publication Date: 2008 Jun PMID: 18353796
Authors: Toyota, H. - Hosokawa, M. - Urabe, I. - Yomo, T.
Journal: Mol Biol Evol

To examine whether a primordial functional protein at the early stages of evolution has structural features, we carried out experimental evolution consisting of 25 cycles (generations) of mutation and selection toward DNA-binding function using a random-sequence polypeptide of 139 amino acid residues with no secondary structure as the initial sequence. In each generation, 16 clones were sampled arbitrarily for sequence analysis, and a phylogenetic tree was constructed. Polypeptide evolution proceeded from the initial point on branch I in 2 main directions of branches II and III. The initial and 2 evolved polypeptides (one at the 24th generation on branch III and the other at the 25th generation on branch II) were purified to examine their functional and structural properties. Although binding of the initial polypeptide to the target DNA was not detected by surface plasmon resonance measurements, the 2 evolved polypeptides bound to the DNA with dissociation constants of 1.6 and 1.0 microM, respectively, indicating an increase in affinity during the experimental evolution. Circular dichroism spectra of the evolved polypeptides, but not of the initial polypeptide, showed features characteristic of the polyproline II (PPII)-like structure, a left-handed helical structure commonly found in natural proteins, suggesting that the structure emerged through the experimental evolution. The same structural feature was found in another experimental evolution toward catalytic activity. These results demonstrate that the PPII-like structure is one of the common features that could have appeared in the early evolutionary stages of primordial functional protein.

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On the expansion of the pentatricopeptide repeat gene family in plants.

Publication Date: 2008 Jun PMID: 18343892
Authors: O'Toole, N. - Hattori, M. - Andres, C. - Iida, K. - Lurin, C. - Schmitz-Linneweber, C. - Sugita, M. - Small, I.
Journal: Mol Biol Evol

Pentatricopeptide repeat (PPR) proteins form a huge family in plants (450 members in Arabidopsis and 477 in rice) defined by tandem repetitions of characteristic sequence motifs. Some of these proteins have been shown to play a role in posttranscriptional processes within organelles, and they are thought to be sequence-specific RNA-binding proteins. The origins of this family are obscure as they are lacking from almost all prokaryotes, and the spectacular expansion of the family in land plants is equally enigmatic. In this study, we investigate the growth of the family in plants by undertaking a genome-wide identification and comparison of the PPR genes of 3 organisms: the flowering plants Arabidopsis thaliana and Oryza sativa and the moss Physcomitrella patens. A large majority of the PPR genes in each of the flowering plants are intron less. In contrast, most of the 103 PPR genes in Physcomitrella are intron rich. A phylogenetic comparison of the PPR genes in all 3 species shows similarities between the intron-rich PPR genes in Physcomitrella and the few intron-rich PPR genes in higher plants. Intron-poor PPR genes in all 3 species also display a bias toward a position of their introns at their 5' ends. These results provide compelling evidence that one or more waves of retrotransposition were responsible for the expansion of the PPR gene family in flowering plants. The differing numbers of PPR proteins are highly correlated with differences in organellar RNA editing between the 3 species.

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Mobility pathways for vertebrate L1, L2, CR1, and RTE clade retrotransposons.

Publication Date: 2008 Jun PMID: 18343891
Authors: Ichiyanagi, K. - Okada, N.
Journal: Mol Biol Evol

Autonomous non-long terminal repeat retrotransposons (NLRs) are ubiquitous mobile genetic elements that insert their DNA copies at new locations by retrotransposition. In vertebrates, there are 4 NLR clades, L1, L2, CR1, and RTE, which diverged in the Precambrian era. It has been demonstrated that retrotransposition of L1 and L2 members proceeds via coordinated reactions of targeted DNA cleavage and reverse transcription catalyzed by the NLR-encoded proteins, which are followed by the joining of the 5' (upstream) junction. However, the study on the mobility pathways for vertebrate NLRs is so far limited to L1 and L2. In this report, using target analysis of nested transposons for genomic copies, we studied retrotransposition pathways for a variety of vertebrate NLRs, including those of the L1, L2, CR1, and RTE clades in the human, cow, opossum, chicken, and zebrafish genomes. Thus, this study constitutes the first comprehensive analysis of NLR retrotransposition products in vertebrates. Our data revealed that these elements share similar mechanisms for the cleavages of the 2 target DNA strands and for the initiation of reverse transcription. Possible endonuclease-independent insertions were also identified. Overall, our results suggest the existence of multiple retrotransposition pathways that are conserved among the diverse NLR clades in various vertebrate hosts.

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Altered miRNA repertoire in the simplified chordate, Oikopleura dioica.

Publication Date: 2008 Jun PMID: 18339653
Authors: Fu, X. - Adamski, M. - Thompson, E. M.
Journal: Mol Biol Evol

Recent studies reveal correlation between microRNA (miRNA) innovation and increased developmental complexity. This is exemplified by dramatic expansion of the miRNA inventory in vertebrates, a lineage where genome duplication has played a significant evolutionary role. Urochordates, the closest extant group to the vertebrates, exhibit an opposite trend to genome and morphological simplification. We show that the urochordate, larvacean, Oikopleura dioica, possesses the requisite miRNA biogenic machinery. The miRNAs isolated by small RNA cloning were expressed throughout the short life cycle, a number of which were stocked as maternal determinants prior to rapid embryonic development. We identify sex-specific miRNAs that appeared as male/female gonad differentiation became apparent and were maintained throughout spermatogenesis. Whereas 80% of mammalian miRNAs are hosted in introns of protein-coding genes, the majority of O. dioica miRNA loci were located in antisense orientations to such genes. Including sister group ascidians in analysis of the urochordate miRNA repertoire, we find that 11 highly conserved bilaterian miRNA families have been lost or derived to the point they are not recognizable in urochordates and a further 4 of these families are absent in larvaceans. Subsequent to this loss/derivation, at least 29 novel miRNA families have been acquired in larvaceans. This suggests a profound reorganization of the miRNA repertoire integral to evolution in the urochordate lineage.

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Two circular chromosomes of unequal copy number make up the mitochondrial genome of the rotifer Brachionus plicatilis.

Publication Date: 2008 Jun PMID: 18326862
Authors: Suga, K. - Mark Welch, D. B. - Tanaka, Y. - Sakakura, Y. - Hagiwara, A.
Journal: Mol Biol Evol

The monogonont rotifer Brachionus plicatilis is an emerging model system for a diverse array of questions in limnological ecosystem dynamics, the evolution of sexual recombination, cryptic speciation, and the phylogeny of basal metazoans. We sequenced the complete mitochondrial genome of B. plicatilis sensu strictu NH1L and found that it is composed of 2 circular chromosomes, designated mtDNA-I (11,153 bp) and mtDNA-II (12,672 bp). Hybridization to DNA isolated from mitochondria demonstrated that mtDNA-I is present at 4 times the copy number of mtDNA-II. The only nucleotide similarity between the 2 chromosomes is a 4.9-kbp region of 99.5% identity including a transfer RNA (tRNA) gene and an extensive noncoding region that contains putative D-loop and control sequence. The mtDNA-I chromosome encodes 4 proteins (ATP6, COB, NAD1, and NAD2), 13 tRNAs, and the large and small subunit ribosomal RNAs; mtDNA-II encodes 8 proteins (COX1-3, NAD3-6, and NAD4L) and 9 tRNAs. Gene order is not conserved between B. plicatilis and its closest relative with a sequenced mitochondrial genome, the acanthocephalan Leptorhynchoides thecatus, or other sequenced mitochondrial genomes. Polymerase chain reaction assays and Southern hybridization to DNA from 18 strains of Brachionus suggest that the 2-chromosome structure has been stable for millions of years. The novel organization of the B. plicatilis mitochondrial genome into 2 nearly equal chromosomes of 4-fold different copy number may provide insight into the evolution of metazoan mitochondria and the phylogenetics of rotifers and other basal animal phyla.

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A mixed branch length model of heterotachy improves phylogenetic accuracy.

Publication Date: 2008 Jun PMID: 18319244
Authors: Kolaczkowski, B. - Thornton, J. W.
Journal: Mol Biol Evol

Evolutionary relationships are typically inferred from molecular sequence data using a statistical model of the evolutionary process. When the model accurately reflects the underlying process, probabilistic phylogenetic methods recover the correct relationships with high accuracy. There is ample evidence, however, that models commonly used today do not adequately reflect real-world evolutionary dynamics. Virtually all contemporary models assume that relatively fast-evolving sites are fast across the entire tree, whereas slower sites always evolve at relatively slower rates. Many molecular sequences, however, exhibit site-specific changes in evolutionary rates, called "heterotachy." Here we examine the accuracy of 2 phylogenetic methods for incorporating heterotachy, the mixed branch length model--which incorporates site-specific rate changes by summing likelihoods over multiple sets of branch lengths on the same tree--and the covarion model, which uses a hidden Markov process to allow sites to switch between variable and invariable as they evolve. Under a variety of simple heterogeneous simulation conditions, the mixed model was dramatically more accurate than homotachous models, which were subject to topological biases as well as biases in branch length estimates. When data were simulated with strong versions of the types of heterotachy observed in real molecular sequences, the mixed branch length model was more accurate than homotachous techniques. Analyses of empirical data sets confirmed that the mixed branch length model can improve phylogenetic accuracy under conditions that cause homotachous models to fail. In contrast, the covarion model did not improve phylogenetic accuracy compared with homotachous models and was sometimes substantially less accurate. We conclude that a mixed branch length approach, although not the solution to all phylogenetic errors, is a valuable strategy for improving the accuracy of inferred trees.

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Long-term evolutionary stability of bacterial endosymbiosis in curculionoidea: additional evidence of symbiont replacement in the dryophthoridae family.

Publication Date: 2008 May PMID: 18310662
Authors: Conord, C. - Despres, L. - Vallier, A. - Balmand, S. - Miquel, C. - Zundel, S. - Lemperiere, G. - Heddi, A.
Journal: Mol Biol Evol

Bacterial intracellular symbiosis (endosymbiosis) is well documented in the insect world where it is believed to play a crucial role in adaptation and evolution. However, although Coleopteran insects are of huge ecological and economical interest, endosymbiont molecular analysis is limited to the Dryophthoridae family. Here, we have analyzed the intracellular symbiotic bacteria in 2 Hylobius species belonging to the Molytinae subfamily (Curculionoidea superfamily) that exhibit different features from the Dryophthoridae insects in terms of their ecology and geographical spanning. Fluorescence in situ hybridization has shown that both Hylobius species harbor rod-shaped pleiomorphic symbiotic bacteria in the oocyte and in the bacteria-bearing organ (the bacteriome), with a shape and location similar to those of the Dryophthoridae bacteriome. Phylogenetic analysis of the 16S ribosomal DNA gene sequences, using the heterogeneous model of DNA evolution, has placed the Hylobius spp. endosymbionts (H-group) at the basal position of the ancestral R-clade of Dryophthoridae endosymbionts named Candidatus Nardonella but relatively distant from the S-clade of Sitophilus spp. endosymbionts. Endosymbionts from the H-group and the R-clade evolved more quickly compared with free-living enteric bacteria and endosymbionts from the S- and D-clades of Dryophthoridae. They are AT biased (58.3% A + T), and they exhibit AT-rich insertions at the same position as previously described in the Candidatus Nardonella 16S rDNA sequence. Moreover, the host phylogenetic tree based on the mitochondrial COI gene was shown to be highly congruent with the H-group and the R-clade, the divergence of which was estimated to be around 125 MYA. These new molecular data show that endosymbiosis is old in Curculionids, going back at least to the common ancestor of Molytinae and Dryophthoridae, and is evolutionary stable, except in 2 Dryophthoridae clades, providing additional and independent supplementary evidence for endosymbiont replacement in these taxa.

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Evolution of the insulin receptor family and receptor isoform expression in vertebrates.

Publication Date: 2008 Jun PMID: 18310661
Authors: Hernandez-Sanchez, C. - Mansilla, A. - de Pablo, F. - Zardoya, R.
Journal: Mol Biol Evol

The molecular phylogeny of the vertebrate insulin receptor (IR) family was reconstructed under maximum likelihood (ML) to establish homologous relationships among its members. A sister group relationship between the orphan insulin-related receptor (IRR) and the insulin-like growth factor 1 receptor (IGF1R) to the exclusion of the IR obtained maximal bootstrap support. Although both IR and IGF1R were identified in all vertebrates, IRR could not be found in any teleost fish. The ancestral character states at each position of the receptor molecule were inferred for IR, IRR + IGF1R, and all 3 paralogous groups based on the recovered phylogeny using ML in order to determine those residues that could be important for the specific function of IR. For 18 residues, ancestral character state of IR was significantly distinct (probability >0.95) with respect to the corresponding inferred ancestral character states both of IRR + IGF1R and of all 3 vertebrate paralogs. Most of these IR distinct (shared derived) residues were located on the extracellular portion of the receptor (because this portion is larger and the rate of generation of IR shared derived sites is uniform along the receptor), suggesting that functional diversification during the evolutionary history of the family was largely generated modifying ligand affinity rather than signal transduction at the tyrosine kinase domain. In addition, 2 residues at positions 436 and 1095 of the human IR sequence were identified as radical cluster-specific sites in IRR + IGF1R. Both Ir and Irr have an extra exon (namely exon 11) with respect to Igf1r. We used the molecular phylogeny to infer the evolution of this additional exon. The Irr exon 11 can be traced back to amphibians, whereas we show that presence and alternative splicing of Ir exon 11 seems to be restricted exclusively to mammals. The highly divergent sequence of both exons and the reconstructed phylogeny of the vertebrate IR family strongly indicate that both exons were acquired independently by each paralog.

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Adaptive evolution of hepcidin genes in antarctic notothenioid fishes.

Publication Date: 2008 Jun PMID: 18310660
Authors: Xu, Q. - Cheng, C. H. - Hu, P. - Ye, H. - Chen, Z. - Cao, L. - Chen, L. - Shen, Y. - Chen, L.
Journal: Mol Biol Evol

Hepcidin is a small bioactive peptide with dual roles as an antimicrobial peptide and as the principal hormonal regulator of iron homeostasis in human and mouse. Hepcidin homologs of very similar structures are found in lower vertebrates, all comprise approximately 20-25 amino acids with 8 highly conserved cysteines forming 4 intramolecular disulfide bonds, giving hepcidin a hairpin structure. Hepcidins are particularly diverse in teleost fishes, which may be related to the diversity of aquatic environments with varying degree of pathogen challenge, oxygenation, and iron concentration, factors known to alter hepcidin expression in mammals. We characterized the diversity of hepcidin genes of the Antarctic notothenioid fishes that are endemic to the world's coldest and most oxygen-rich marine water. Notothenioid fishes have at least 4 hepcidin variants, in 2 distinctive structural types. Type I hepcidins comprise 3 distinct variants that are homologs of the widespread 8-cysteine hepcidins. Type II is a novel 4-cysteine variant and therefore only 2 possible disulfide bonds, highly expressed in hematopoietic tissues. Analyses of d(N)/d(S) substitution rate ratios and likelihood ratio test under site-specific models detected significant signal of positive Darwinian selection on the mature hepcidin-coding sequence, suggesting adaptive evolution of notothenioid hepcidins. Genomic polymerase chain reaction and Southern hybridization showed that the novel type II hepcidin occurs exclusively in lineages of the Antarctic notothenioid radiation but not in the basal non-Antarctic taxa, and lineage-specific positive selection was detected on the branch leading to the type II hepcidin clade under branch-site models, suggesting adaptive evolution of the reduced cysteine variant in response to the polar environment. We also isolated a structurally distinct 4-cysteine (4cys) hepcidin from an Antarctic eelpout that is unrelated to the notothenioids but inhabits the same freezing water. Neighbor-Joining (NJ) analyses of teleost hepcidins showed that the eelpout 4cys variant arose independently from the notothenioid version, which lends support to adaptive evolution of reduced cysteine hepcidin variants on cold selection. The NJ tree also showed taxonomic-specific expansions of hepcidin variants, indicating that duplication and diversification of hepcidin genes play important roles in evolutionary response to diverse ecological conditions.

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Conserved features and evolutionary shifts of the EDA signaling pathway involved in vertebrate skin appendage development.

Publication Date: 2008 May PMID: 18304980
Authors: Pantalacci, S. - Chaumot, A. - Benoit, G. - Sadier, A. - Delsuc, F. - Douzery, E. J. - Laudet, V.
Journal: Mol Biol Evol

It is widely accepted that evolutionary changes in conserved developmental signaling pathways play an important role in morphological evolution. However, few in silico studies were interested in tracking such changes in a signaling pathway. The Ectodysplasin (EDA) pathway provides an opportunity to fill this gap because it is involved in vertebrate skin appendage development such as scales, teeth, hair, and feathers that take an obvious part in the adaptation of species to their environment. We benefited from the large amount of genomic data now available to explore the evolution of the upstream genes of the EDA pathway. In mammals, these genes are eda (encoding 2 ligands, EDA-A1 and EDA-A2), edar (EDA-A1 receptor), edaradd (EDA receptor [EDAR] adapter), xedar (EDA-A2 receptor), and troy (a XEDAR-related receptor). We show that the evolution of EDA pathway genes combines both strongly conserved features and evolutionary shifts. These shifts are found at different signaling levels (from the ligand to intracellular signaling) and at different taxonomic levels (class, suborder, and genera). Although conserved features likely participate to the similarities found in the early development of vertebrate skin appendages, these shifts might account for innovations and specializations. Moreover, our study demonstrates that we can now benefit from the large number of sequenced vertebrate genomes to explore the evolution of specific signaling pathways and thereby to open new perspectives for developmental biology and evolutionary developmental biology.

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Comparative analysis of the MIR319a microRNA locus in Arabidopsis and related Brassicaceae.

Publication Date: 2008 May PMID: 18296705
Authors: Warthmann, N. - Das, S. - Lanz, C. - Weigel, D.
Journal: Mol Biol Evol

MicroRNAs (miRNAs) are important regulators of gene expression in multicellular organisms. Yet, little is known about their molecular evolution. The 20- to 22-nt long miRNAs are processed in plants from foldbacks that are a few hundred base pairs in size. Often, these foldbacks are embedded in much larger precursor transcripts. To investigate functional constraints on sequence evolution of miRNA precursor genes, we have studied sequence variation in the precursor of miR319a, MIR319a, between species from the Brassicaceae. We compared the genomic context in Arabidopsis thaliana, Arabidopsis halleri, and Capsella rubella, using bacterial artificial chromosome clones, and analyzed precursor sequences obtained by polymerase chain reaction from 13 additional species. Phylogenetic shadowing identifies a conserved motif around the transcription start site, which we demonstrate to be functionally important. We further assessed the functionality of MIR319a orthologs from several Brassicaceae species in A. thaliana. The ortholog from kale (Brassica oleracea var. acephala) was found to be largely inactive, at least partially due to mutations in the miRNA itself, but experimental evidence suggests that loss of miR319a function is compensated by other members of the miR319 family. More broadly, we find that the foldback diverges less rapidly than the remainder of the primary transcript. To understand the molecular evolution of miRNA genes, investigations at different levels of phylogenetic divergence are required.

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Overdominance in the human genome and olfactory receptor activity.

Publication Date: 2008 May PMID: 18296703
Authors: Alonso, S. - Lopez, S. - Izagirre, N. - de la Rua, C.
Journal: Mol Biol Evol

We investigate the contribution of overdominance to the maintenance of polymorphism in the human genome during the recent evolution of our species. Using the HapMap genotypic information, we have detected that the Gene Ontology term "olfactory receptor activity" is a molecular function overrepresented in genes that have SNPs (Single Nucleotide Polymorphisms) showing higher than expected number of heterozygotes in the HapMap populations. Our results suggest that the diversity of a subset of human olfactory receptors (ORs) may have been maintained by balancing selection, in the form of overdominance. This observation may suggest that the loss of OR genes during the evolution of the human lineage may have been accompanied by an increased capability to discriminate odorants with closely similar structures.

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Adaptive evolution of newly emerged micro-RNA genes in Drosophila.

Publication Date: 2008 May PMID: 18296702
Authors: Lu, J. - Fu, Y. - Kumar, S. - Shen, Y. - Zeng, K. - Xu, A. - Carthew, R. - Wu, C. I.
Journal: Mol Biol Evol

How often micro-RNA (miRNA) genes emerged and how fast they evolved soon after their emergence are some of the central questions in the evolution of miRNAs. Because most known miRNA genes are ancient and highly conserved, these questions can be best answered by identifying newly emerged miRNA genes. Among the 78 miRNA genes in Drosophila reported before 2007, only 5 are confirmed to be newly emerged in the genus (although many more can be found in the newly reported data set; e.g., Ruby et al. 2007; Stark et al. 2007; Lu et al. 2008). These new miRNA genes have undergone numerous changes, even in the normally invariant mature sequences. Four of them (the miR-310/311/312/313 cluster, denoted miR-310s) were duplicated from other conserved miRNA genes. The fifth one (miR-303) appears to be a very young gene, originating de novo from a non-miRNA sequence recently. We sequenced these 5 miRNA genes and their neighboring regions from a worldwide collection of Drosophila melanogaster lines. The levels of divergence and polymorphism in these miRNA genes, vis-a-vis those of the neighboring DNA sequences, suggest that these 5 genes are evolving adaptively. Furthermore, the polymorphism pattern of miR-310s in D. melanogaster is indicative of hitchhiking under positive selection. Thus, a large number of adaptive changes over a long period of time may be essential for the evolution of newly emerged miRNA genes.

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Evolutionary origins of a novel host plant detoxification gene in butterflies.

Publication Date: 2008 May PMID: 18296701
Authors: Fischer, H. M. - Wheat, C. W. - Heckel, D. G. - Vogel, H.
Journal: Mol Biol Evol

Chemical interactions between plants and their insect herbivores provide an excellent opportunity to study the evolution of species interactions on a molecular level. Here, we investigate the molecular evolutionary events that gave rise to a novel detoxifying enzyme (nitrile-specifier protein [NSP]) in the butterfly family Pieridae, previously identified as a coevolutionary key innovation. By generating and sequencing expressed sequence tags, genomic libraries, and screening databases we found NSP to be a member of an insect-specific gene family, which we characterized and named the NSP-like gene family. Members consist of variable tandem repeats, are gut expressed, and are found across Insecta evolving in a dynamic, ongoing birth-death process. In the Lepidoptera, multiple copies of single-domain major allergen genes are present and originate via tandem duplications. Multiple domain genes are found solely within the brassicaceous-feeding Pieridae butterflies, one of them being NSP and another called major allergen (MA). Analyses suggest that NSP and its paralog MA have a unique single-domain evolutionary origin, being formed by intragenic domain duplication followed by tandem whole-gene duplication. Duplicates subsequently experienced a period of relaxed constraint followed by an increase in constraint, perhaps after neofunctionalization. NSP and its ortholog MA are still experiencing high rates of change, reflecting a dynamic evolution consistent with the known role of NSP in plant-insect interactions. Our results provide direct evidence to the hypothesis that gene duplication is one of the driving forces for speciation and adaptation, showing that both within- and whole-gene tandem duplications are a powerful force underlying evolutionary adaptation.

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Heterotypy in the N-terminal region of growth/differentiation factor 5 (GDF5) mature protein during teleost evolution.

Publication Date: 2008 May PMID: 18296700
Authors: Fujimura, K. - Terai, Y. - Ishiguro, N. - Miya, M. - Nishida, M. - Okada, N.
Journal: Mol Biol Evol

Heterotypy is now recognized as a generative force in the formation of new proteins through modification of existing proteins. We report that heterotypy in the N-terminal region of the mature growth/differentiation factor 5 (GDF5) protein occurred during evolution of teleosts. N-terminal length variation of GDF5 was found among teleost interfamilies and interorders but not within teleost families or among tetrapods. We further show that increase of proline and glutamine to the N-terminal region of mature GDF5 occurred in Eurypterygii, the higher lineage of teleosts. Because the basic amino acids, believed to control diffusion, are conserved in this region across all species examined, we suggest that the N-terminal elongation of the mature GDF5 protein during evolution has altered the protein diffusion in Eurypterygii, leading to high concentrations of the protein in the joint of the pharyngeal skeleton, the location of cartilage formation during development.

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Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes.

Publication Date: 2008 May PMID: 18296699
Authors: Masta, S. E. - Boore, J. L.
Journal: Mol Biol Evol

The cloverleaf secondary structure of transfer RNA (tRNA) is highly conserved across all forms of life. Here, we provide sequence data and inferred secondary structures for all tRNA genes from 8 new arachnid mitochondrial genomes, including representatives from 6 orders. These data show remarkable reductions in tRNA gene sequences, indicating that T-arms are missing from many of the 22 tRNAs in the genomes of 4 out of 7 orders of arachnids. Additionally, all opisthothele spiders possess some tRNA genes that lack sequences that could form well-paired aminoacyl acceptor stems. We trace the evolution of T-arm loss onto phylogenies of arachnids and show that a genome-wide propensity to lose sequences that encode canonical cloverleaf structures likely evolved multiple times within arachnids. Mapping of structural characters also shows that certain tRNA genes appear more evolutionarily prone to lose the sequence coding for the T-arm and that once a T-arm is lost, it is not regained. We use tRNA structural data to construct a phylogeny of arachnids and find high bootstrap support for a clade that is not supported in phylogenies that are based on more traditional morphological characters. Together, our data demonstrate variability in structural evolution among different tRNAs as well as evidence for parallel evolution of the loss of sequence coding for tRNA arms within an ancient and diverse group of animals.

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The preferential retention of starch synthesis genes reveals the impact of whole-genome duplication on grass evolution.

Publication Date: 2008 Jun PMID: 18296698
Authors: Wu, Y. - Zhu, Z. - Ma, L. - Chen, M.
Journal: Mol Biol Evol

Gene duplication is a major force in evolution. Here, we analyzed the fate of duplicated genes following the ancient whole-genome duplication (WGD) in rice. Polyploidy-derived duplicated genes were found to be preferentially lost from one of each pair of duplicated chromosomal segments, suggesting that the asymmetric gene loss may result from transcriptome dominance of the ancestral allotetraploid genome. Genes involved in synthesis and catabolism of saccharides were found to be preferentially retained in rice, reflecting different trajectories of duplicated genes formed by polyploidy between rice and Arabidopsis. Further studies demonstrated all 3 catalyzing steps in the starch biosynthesis pathway have polyploidy-derived duplicated genes and one copy in each step forms a dominant pathway in the grain filling-stage rice. The new starch biosynthesis pathway reflects one aspect of the impact of WGD on grass evolution.

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Ancient DNA identification of early 20th century simian T-cell leukemia virus type 1.

Publication Date: 2008 Jun PMID: 18296697
Authors: Calvignac, S. - Terme, J. M. - Hensley, S. M. - Jalinot, P. - Greenwood, A. D. - Hanni, C.
Journal: Mol Biol Evol

The molecular identification of proviruses from ancient tissues (and particularly from bones) remains a contentious issue. It can be expected that the copy number of proviruses will be low, which magnifies the risk of contamination with retroviruses from exogenous sources. To assess the feasibility of paleoretrovirological studies, we attempted to identify proviruses from early 20th century bones of museum specimens while following a strict ancient DNA methodology. Simian T-cell leukemia virus type 1 sequences were successfully obtained and authenticated from a Chlorocebus pygerythrus specimen. This represents the first clear evidence that it will be possible to use museum specimens to better characterize simian and human T-tropic retrovirus genetic diversity and analyze their origin and evolution, in greater detail.

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Evolution of gene expression in the Drosophila olfactory system.

Publication Date: 2008 Jun PMID: 18296696
Authors: Kopp, A. - Barmina, O. - Hamilton, A. M. - Higgins, L. - McIntyre, L. M. - Jones, C. D.
Journal: Mol Biol Evol

Host plant shifts by phytophagous insects play a key role in insect evolution and plant ecology. Such shifts often involve major behavioral changes as the insects must acquire an attraction and/or lose the repulsion to the new host plant's odor and taste. The evolution of chemotactic behavior may be due, in part, to gene expression changes in the peripheral sensory system. To test this hypothesis, we compared gene expression in the olfactory organs of Drosophila sechellia, a narrow ecological specialist that feeds on the fruit of Morinda citrifolia, with its close relatives Drosophila simulans and Drosophila melanogaster, which feed on a wide variety of decaying plant matter. Using whole-genome microarrays and quantitative polymerase chain reaction, we surveyed the entire repertoire of Drosophila odorant receptors (ORs) and odorant-binding proteins (OBPs) expressed in the antennae. We found that the evolution of OR and OBP expression was accelerated in D. sechellia compared both with the genome average in that species and with the rate of OR and OBP evolution in the other species. However, some of the gene expression changes that correlate with D. sechellia's increased sensitivity to Morinda odorants may predate its divergence from D. simulans. Interspecific divergence of olfactory gene expression cannot be fully explained by changes in the relative abundance of different sensilla as some ORs and OBPs have evolved independently of other genes expressed in the same sensilla. A number of OR and OBP genes are upregulated in D. sechellia compared with its generalist relatives. These genes include Or22a, which likely responds to a key odorant of M. citrifolia, and several genes that are yet to be characterized in detail. Increased expression of these genes in D. sechellia may have contributed to the evolution of its unique chemotactic behavior.

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Near intron positions are reliable phylogenetic markers: an application to holometabolous insects.

Publication Date: 2008 May PMID: 18296416
Authors: Krauss, V. - Thummler, C. - Georgi, F. - Lehmann, J. - Stadler, P. F. - Eisenhardt, C.
Journal: Mol Biol Evol

Today, the reconstruction of the organismal evolutionary tree is based mainly on molecular sequence data. However, sequence data are sometimes insufficient to reliably resolve in particular deep branches. Thus, it is highly desirable to find novel, more reliable types of phylogenetic markers that can be derived from the wealth of genomic data. Here, we consider the gain of introns close to older preexisting ones. Because correct splicing is impeded by very small exons, nearby pairs of introns very rarely coexist, that is, the gain of the new intron is nearly always associated with the loss of the old intron. Both events may even be directly connected as in cases of intron migration. Therefore, it should be possible to identify one of the introns as ancient (plesiomorphic) and the other as novel (derived or apomorphic). To test the suitability of such near intron pairs (NIPs) as a marker class for phylogenetic analysis, we undertook an analysis of the evolutionary positions of bees and wasps (Hymenoptera) and beetles (Coleoptera) in relation to moths (Lepidoptera) and dipterans (Diptera) using recently completed genome project data. By scanning 758 putatively orthologous gene structures of Apis mellifera (Hymenoptera) and Tribolium castaneum (Coleoptera), we identified 189 pairs of introns, one from each species, which are located less than 50 nt from each other. A comparison with genes from 5 other holometabolan and 9 metazoan outgroup genomes resulted in 22 shared derived intron positions found in beetle as well as in butterflies and/or dipterans. This strongly supports a basal position of hymenopterans in the holometabolous insect tree. In addition, we found 31 and 12 intron positions apomorphic for A. mellifera and T. castaneum, respectively, which seem to represent changes inside these branches. Another 12 intron pairs indicate parallel intron gains or extraordinarily small exons. In conclusion, we show here that the analysis of phylogenetically nested, nearby intron pairs is suitable to identify evolutionarily younger intron positions and to determine their relative age, which should be of equal importance for the understanding of intron evolution and the reconstruction of the eukaryotic tree.

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Extremely intron-rich genes in the alveolate ancestors inferred with a flexible maximum-likelihood approach.

Publication Date: 2008 May PMID: 18296415
Authors: Csuros, M. - Rogozin, I. B. - Koonin, E. V.
Journal: Mol Biol Evol

Chromalveolates are a large, diverse supergroup of unicellular eukaryotes that includes Apicomplexa, dinoflagellates, ciliates (three lineages that form the alveolate branch), heterokonts, haptophytes, and cryptomonads (three lineages comprising the chromist branch). All sequenced genomes of chromalveolates have relatively low intron density in protein-coding genes, and few intron positions are shared between chromalveolate lineages. In contrast, genes of different chromalveolates share many intron positions with orthologous genes from other eukaryotic supergroups, in particular, the intron-rich orthologs from animals and plants. Reconstruction of the history of intron gain and loss during the evolution of chromalveolates using a general and flexible maximum-likelihood approach indicates that genes of the ancestors of chromalveolates and, particularly, alveolates had unexpectedly high intron densities. It is estimated that the chromalveolate ancestor had, approximately, two-third of the human intron density, whereas the intron density in the genes of the alveolate ancestor is estimated to be slightly greater than the human intron density. Accordingly, it is inferred that the evolution of chromalveolates was dominated by intron loss. The conclusion that ancestral chromalveolate forms had high intron densities is unexpected because all extant unicellular eukaryotes have relatively few introns and are thought to be unable to maintain numerous introns due to intense purifying selection in their, typically, large populations. It is suggested that, at early stages of evolution, chromalveolates went through major population bottlenecks that were accompanied by intron invasion.

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A test of the null model for 5' UTR evolution based on GC content.

Publication Date: 2008 May PMID: 18296414
Authors: Reuter, M. - Engelstadter, J. - Fontanillas, P. - Hurst, L. D.
Journal: Mol Biol Evol

Eukaryotic mRNAs are headed by a stretch of noncoding sequence, the 5' untranslated region (UTR). It has been proposed that the length of 5' UTRs is selectively neutral and evolves under a process of stochastic destruction and recruitment of core promoter elements, combined with selection against the premature initiation of translation. We test this null model by investigating whether 5' UTR length varies with genomic GC content, an implicit prediction of the model. Using simulations, we show that the null model predicts a positive relationship between GC content and UTR length for genes regulated by a TATA box. Although this prediction is borne out qualitatively in genomic data from yeast, fruit flies, and humans, we find marked quantitative discrepancies. We conclude that UTR length may be shaped to some degree by the forces considered in the null model but that the model fails to provide a complete explanation for UTR length evolution.

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Genesis and expansion of metazoan transcription factor gene classes.

Publication Date: 2008 May PMID: 18296413
Authors: Larroux, C. - Luke, G. N. - Koopman, P. - Rokhsar, D. S. - Shimeld, S. M. - Degnan, B. M.
Journal: Mol Biol Evol

We know little about the genomic events that led to the advent of a multicellular grade of organization in animals, one of the most dramatic transitions in evolution. Metazoan multicellularity is correlated with the evolution of embryogenesis, which presumably was underpinned by a gene regulatory network reliant on the differential activation of signaling pathways and transcription factors. Many transcription factor genes that play critical roles in bilaterian development largely appear to have evolved before the divergence of cnidarian and bilaterian lineages. In contrast, sponges seem to have a more limited suite of transcription factors, suggesting that the developmental regulatory gene repertoire changed markedly during early metazoan evolution. Using whole-genome information from the sponge Amphimedon queenslandica, a range of eumetazoans, and the choanoflagellate Monosiga brevicollis, we investigate the genesis and expansion of homeobox, Sox, T-box, and Fox transcription factor genes. Comparative analyses reveal that novel transcription factor domains (such as Paired, POU, and T-box) arose very early in metazoan evolution, prior to the separation of extant metazoan phyla but after the divergence of choanoflagellate and metazoan lineages. Phylogenetic analyses indicate that transcription factor classes then gradually expanded at the base of Metazoa before the bilaterian radiation, with each class following a different evolutionary trajectory. Based on the limited number of transcription factors in the Amphimedon genome, we infer that the genome of the metazoan last common ancestor included fewer gene members in each class than are present in extant eumetazoans. Transcription factor orthologues present in sponge, cnidarian, and bilaterian genomes may represent part of the core metazoan regulatory network underlying the origin of animal development and multicellularity.

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Inverted replication of vertebrate mitochondria.

Publication Date: 2008 May PMID: 18296412
Authors: Fonseca, M. M. - Posada, D. - Harris, D. J.
Journal: Mol Biol Evol

After analyzing the base composition asymmetry of coding regions in vertebrate mitochondria, we identified 2 fishes, Albula glossodonta and Bathygadus antrodes, with inverted compositional patterns. Both species appear to have an unusual control region (CR), and in B. antrodes, it has switched from the light strand to the heavy strand. To our knowledge, this is the first report in vertebrates of inverted mitochondrial replication, caused by an inversion of the CR. These findings support the strand-asymmetric model of mtDNA replication and suggest that vertebrate mtDNA can tolerate globally reversed mutational pressures. In addition, we propose that nucleotide bias is not strand specific but that it depends on the location of the CR.

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Identification of novel mammalian caspases reveals an important role of gene loss in shaping the human caspase repertoire.

Publication Date: 2008 May PMID: 18281271
Authors: Eckhart, L. - Ballaun, C. - Hermann, M. - VandeBerg, J. L. - Sipos, W. - Uthman, A. - Fischer, H. - Tschachler, E.
Journal: Mol Biol Evol

Proteases of the caspase family play central roles in apoptosis and inflammation. Recently, we have described a new gene encoding caspase-15 that has been inactivated independently in different mammalian lineages. To determine the dynamics of gene duplication and loss in the entire caspase gene family, we performed a comprehensive evolutionary analysis of mammalian caspases. By comparative genomics and reverse transcriptase-polymerase chain reaction analyses, we identified 3 novel mammalian caspase genes, which we tentatively named caspases-16 through -18. Caspase-16, which is most similar in sequence to caspase-14, has been conserved in marsupials and placental mammals, including humans. Caspase-17, which is most similar to caspase-3, has been conserved among fish, frog, chicken, lizard, and the platypus but is absent from marsupials and placental mammals. Caspase-18, which is most similar to caspase-8, has been conserved among chicken, platypus, and opossum but is absent from placental mammals. These gene distribution patterns suggest that, in the evolutionary lineage leading to humans, caspase-17 was lost after the split of protherian and therian mammals and caspase-18 was lost after the split of marsupials and placental mammals. In the canine genome, the number of caspases has been reduced by the fusion of the neighboring genes caspases-1 and -4, resulting in a single coding region. Further lineage-specific gene inactivations were found for caspase-10 in murine rodents and caspase-12 in humans, rabbit, and cow. Lineage-specific gene duplications were found for caspases-1, -3, and -12 in opossum and caspase-4 in primates. Other caspases were generally conserved in all mammalian species investigated. Using the positions of introns as stable characters during recent vertebrate evolution, we define 3 phylogenetic clades of caspase genes: caspases-1/-2/-4/-5/-9/-12/-14/-15/-16 (clade I), caspases-3/-6/-7/-17 (clade II), and caspases-8/-10/-18/CFLAR (clade III). We conclude that gene inactivations have occurred in each of the 3 caspase clades and that gene loss has been as critical as gene duplication in the evolution of the human repertoire of caspases.

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Calculating bootstrap probabilities of phylogeny using multilocus sequence data.

Publication Date: 2008 May PMID: 18281270
Authors: Seo, T. K.
Journal: Mol Biol Evol

Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data, these methods require heavy computation, and their application is limited to the analysis of a moderate number of genes and taxa. Distance matrix methods present suitable alternatives for analyzing huge amounts of sequence data. However, the manner in which distance methods can be applied to multilocus sequence data remains unknown. Here, we suggest new procedures to estimate molecular phylogeny using multilocus sequence data and evaluate its significance in the framework of the distance method. We found that concatenation of the multilocus sequence data may result in incorrect phylogeny estimation with an extremely high bootstrap probability (BP), which is due to incorrect estimation of the distances and intentional ignorance of the intergene variations. Therefore, we suggest that the distance matrices for multilocus sequence data be estimated separately and these matrices be subsequently combined to reconstruct phylogeny instead of phylogeny reconstruction using concatenated sequence data. To calculate the BPs of the reconstructed phylogeny, we suggest that 2-stage bootstrap procedures be adopted; in this, genes are resampled followed by resampling of the sequence columns within the resampled genes. By resampling the genes during calculation of BPs, intergene variations are properly considered. Via simulation studies and empirical data analysis, we demonstrate that our 2-stage bootstrap procedures are more suitable than the conventional bootstrap procedure that is adopted after sequence concatenation.

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Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals.

Publication Date: 2008 May PMID: 18281269
Authors: Glazov, E. A. - McWilliam, S. - Barris, W. C. - Dalrymple, B. P.
Journal: Mol Biol Evol

MicroRNAs (miRNAs) are a rapidly growing family of small regulatory RNAs modulating gene expression in plants and animals. In animals, most of the miRNAs discovered in early studies were found to be evolutionarily conserved across the whole kingdom. More recent studies, however, have identified many miRNAs that are specific to a particular group of organisms or even a single species. These present a question about evolution of the individual miRNAs and their role in establishing and maintaining lineage-specific functions and characteristics. In this study, we describe a detailed analysis of the miRNA cluster (hereafter mir-379/mir-656 cluster) located within the imprinted DLK-DIO3 region on human chromosome 14. We show that orthologous miRNA clusters are present in all sequenced genomes of the placental (eutherian) mammals but not in the marsupial (metatherian), monotreme (prototherian), or any other vertebrate genomes. We provide evidence that the locus encompassing this cluster emerged in an early eutherian ancestor prior to the radiation of modern placental mammals by tandem duplication of the ancient precursor sequence. The original amplified cluster may have contained in excess of 250 miRNA precursor sequences, most of which now appear to be inactive. Examination of the eutherian genomes showed that the cluster has been maintained in evolution for approximately 100 Myr. Analysis of genes that contain predicted evolutionarily conserved targets for miRNAs from this cluster revealed significant overrepresentation of the Gene Ontology terms associated with biological processes such as neurogenesis, embryonic development, transcriptional regulation, and RNA metabolism. Consistent with these findings, a survey of the miRNA expression data within the cluster demonstrates a strong bias toward brain and placenta samples from adult organisms and some embryonic tissues. Our results suggest that emergence of the mir-379/mir-656 miRNA cluster was one of the factors that facilitated evolution of the placental mammals. Overrepresentation of genes involved in regulation of neurogenesis among predicted miRNAs targets indicates an important role of the mir-379/mir-656 cluster in this biological process in the placental mammals.

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