Molecular Biology and Evolution - Advance Access

Nucleus-encoded periplastid-targeted EFL in chlorarachniophytes

Gile, G. H., Keeling, P. J. — 2008-07-03

Chlorarachniophytes are cercozoan amoeboflagellates that acquired photosynthesis by enslaving a green alga, which has retained a highly reduced nucleus called a nucleomorph. The nucleomorph lacks many genes necessary for its own maintenance and expression, suggesting that some genes have been moved to the host nucleus and their products are now targeted back to the periplastid compartment (PPC), the reduced eukaryotic cytoplasm of the endosymbiont. Protein trafficking in chlorarachniophytes is therefore complex, including nucleus-encoded plastid-targeted proteins, nucleomorph-encoded plastid-targeted proteins, and nucleus-encoded periplastid-targeted proteins. A major gap in our understanding of this system is the PPC-targeted proteins, since none have been described in any chlorarachniophytes. Here we describe the first such protein, the GTPase EFL. EFL was characterized from seven chlorarachniophytes and two distinct types were found. One is related to foraminiferan EFL and lacks an amino-terminal extension. The second, distantly related, type encodes an amino-terminal extension consisting of a signal peptide followed by sequence sharing many characteristics with transit peptides from nucleus-encoded plastid-targeted proteins, and which we conclude is most likely PPC-targeted. Western blotting with antibodies specific to putative host and PPC-targeted EFL from the chlorarachniophytes Bigelowiella natans and Gymnochlora stellata is consistent with post-translational cleavage of the leaders from PPC-targeted proteins. Immunolocalization of both proteins in B. natans confirmed the cytosolic location of the leaderless EFL and a distinct localization pattern for the PPC-targeted protein, but could not rule out a plastid location (albeit very unlikely). We sought other proteins with a similar leader and identified a eukaryotic translation initiation factor-1 encoding a bipartite extension with the same properties. Transit peptide sequences were characterized from all three classes of targeted protein by comparing all examples of each class from expressed sequence tag (EST) surveys of B. natans and G. stellata. No recognizable difference between plastid- and PPC-targeted proteins was observed, but nucleomorph-encoded transit peptides differ, likely reflecting high AT content of nucleomorph genomes. Taken together, the data suggest that the system that directs proteins to the PPC in chlorarachniophytes uses a bipartite targeting sequence, as does the PPC-targeting system that evolved independently in cryptomonads.

Gene Expansion and Retention Leads to A Diverse Tyrosine Kinase Superfamily in Amphioxus

2008-07-03

Tyrosine kinase (TK) proteins play a central role in cellular behavior and development of animals. The expansion of this superfamily is regarded as a key event in the evolution of the complex signaling pathways and gene networks of metazoans, and is a prominent example of how shuffling of protein modules may generate molecular novelties. Using the intron/exon structure within the TK domain (‘TK intron code’) as a complementary tool for the assignment of orthology and paralogy, we identified and studied the 118 TK proteins of the amphioxus Branchiostoma floridae genome to elucidate TK gene family evolution in metazoans and chordates in particular. Unlike all characterized metazoans to date, amphioxus has members of all known widespread TK families, with not a single loss. Putting amphioxus TKs in an evolutionary context, including new data from the cnidarian Nematostella vectensis, the echinoderm Strongylocentrotus purpuratus and the ascidian Ciona intestinalis, we suggest new evolutionary histories for different TK families, and draw a new global picture of gene loss/gain in the different phyla. Surprisingly, our survey also detected an unprecedented expansion of a group of closely related TK families, including TIE, FGFR, PDGFR and RET, due most probably to massive gene duplication and exon shuffling. Based on their highly similar intron/exon structure at the TK domain, we suggest that this group of TK families constitute a superfamily of TK proteins, which we termed EXTK (EXpanded TK), after their seemingly unique propensity to gene duplication and exon shuffling, not only in amphioxus, but across all metazoan groups. Due to this extreme tendency to both retention and expansion of TK genes, amphioxus harbors the richest and most diverse TK repertoire among all metazoans studied so far, retaining most of the gene complement of its ancestors, but having evolved its own repertoire of genetic novelties.

Likelihood Based Clustering (LiBaC) for Codon Models, a method for grouping sites according to similarities in the underlying process of evolution

Bao, L., Gu, H., Dunn, K. A., Bielawski, J. P. — 2008-06-26

Models of codon evolution are useful for investigating the strength and direction of natural selection via a parameter for the nonsynonymous/synonymous rate ratio ( = d_N /d_S). Different codon models are available to account for diversity of the evolutionary patterns among sites. Codon models which specify data partitions as fixed effects allow the most evolutionary diversity among sites, but require that sites-partitions are a priori identifiable. Models which use a parametric distribution to express the variability in the ratio across sites do not require a priori partitioning of sites, but they permit less among-site diversity in the evolutionary process. Simulation studies presented in this paper indicate that differences among sites in estimates of under an overly simplistic analytical model can reflect more than just natural selection pressure. We also find that the classic LRTs for positive selection have a high false positive rate in some situations. In this paper we developed a new method for assigning codon sites into groups where each group has a different model, and the likelihood over all sites is maximized. The method, called Likelihood Based Clustering (LiBaC), can be viewed as a generalization of the family of Model Based Clustering (MBC) approaches to models of codon evolution. We report the performance of several LiBaC-based methods, and selected alternative methods, over a wide variety of scenarios. We find that LiBaC, under an appropriate model, can provide reliable parameter estimates when the process of evolution is very heterogeneous among groups of sites. Certain types of proteins, such as transmembrane proteins, are expected to exhibit such heterogeneity. A survey of genes encoding transmembrane proteins suggests that overly-simplistic models could be leading to false signal for positive selection among such genes. In these cases, LiBaC-based methods offer an important addition to a "tool box" of methods thereby helping to uncover robust evidence for the action of positive selection.

Analysis Of A Horizontally Transferred Pathway Involved In Vitamin B6 Biosynthesis From The Soybean Cyst Nematode Heterodera glycines

Craig, J. P., Bekal, S., Hudson, M., Domier, L., Niblack, T., Lambert, K. N. — 2008-06-26

Heterodera glycines is an obligate plant parasite capable of biochemically and developmentally altering its host's cells in order to create a specialized feeding cell. Although the exact mechanism of feeding cell morphogenesis remains a mystery, the nematode's ability to manipulate the plant is thought to be due in part to horizontally transferred genes (HGT). A bioinformatic screen of the nematode genome has revealed homologues of the genes SNZ and SNO, which comprise a metabolic pathway for the de novo biosynthesis of pyridoxal 5’phosphate (PLP), the active form of vitamin B₆. Analysis of the two genes, HgSNZ and HgSNO, show that they contain nematode-like introns, generate polyadenylated mRNAs, and map to the SCN genetic linkage map, indicating they are part of the nematode genome. However, gene synteny, protein homology, and phylogenetic evidence suggest prokaryotic origin. This would represent the first case of the horizontal gene transfer of a complete pathway into a nematode or terrestrial animal. Vitamin B₆ acts as a cofactor in over 140 different enzymes and recent studies point towards an important role as a potent quencher of reactive oxygen species (ROS). With H. glycines’ penchant for acquiring parasitism genes through HGT along with the absence of this pathway in other land-based animals suggests a specific need for vitamin B₆ which may involve the parasite-host interaction.

Frequent and Widespread Parallel Evolution of Protein Sequences

Rokas, A., Carroll, S. B. — 2008-06-25

Understanding the patterns and causes of protein sequence evolution is a major challenge in evolutionary biology. One of the critical unresolved issues is the relative contribution of selection and genetic drift to the fixation of amino acid sequence differences between species. Molecular homoplasy, the independent evolution of the same amino acids at orthologous sites in different taxa, is one potential signature of selection, however, relatively little is known about its prevalence in eukaryotic proteomes. To quantify the extent and type of homoplasy among evolving proteins, we used phylogenetic methodology to analyze eight genome-scale data matrices from clades of different evolutionary depths that span the eukaryotic tree of life. We found that the frequency of homoplastic amino acid substitutions in eukaryotic proteins was more than 2-fold higher than expected under neutral models of protein evolution. The overwhelming majority of homoplastic substitutions were parallelisms that involved the most frequently exchanged amino acids with similar physicochemical properties and that could be reached by a single mutational step. We conclude that the role of homoplasy in shaping the protein record is much larger than generally assumed, and we suggest that its high frequency can be explained by both weak positive selection for certain substitutions and purifying selection that constrains substitutions to a small number of functionally equivalent amino acids.

An assessment of the impacts of molecular oxygen on the evolution of proteomes

Vieira-Silva, S., Rocha, E. P. C. — 2008-06-25

Oxygen is one of life's essential elements, but also a source of protein damage, mutagenesis and ageing. Many proteome adaptations have been proposed to tackle such stresses and we assessed them using comparative genomics in a phylogenetic context. Firstly, we find that aerobiosis is a trait with important phylogenetic inertia, but that oxygen content in proteins isn't. Instead, oxygen content is close to the expected values given nucleotide composition. Accordingly, we find no evidence of oxygen being a scarce resource for protein synthesis even among anaerobes. Secondly, we searched for counter-selection of amino acids more prone to oxidation among aerobes. Only cysteine follows the expected trend while triptophan follows the inverse one. When analyzing composition in the context of protein structures and residue accessibility we find that all oxidable residues are avoided at the surface of proteins. Yet, there is no difference between aerobes and anaerobes in this respect and the effect might be explained by the hydrophobicity of these residues. Thirdly, we revisited the hypothesis that atmospheric enrichment in molecular oxygen led to the development of the communication capabilities of eukaryotes. With a larger dataset and adequate controls, we confirm the trend of longer oxygen-rich outer domains in transmembrane proteins of eukaryotes. Yet, we find no significant association between oxygen concentration in the environment and this trait within prokaryotes, suggesting that this difference is clade-specific and independent of oxygen availability. We find that genes involved in cellular responses to oxygen are much more frequent among aerobes and we suggest that they erase most expected differences in terms of proteome composition between organisms facing high and low oxygen concentrations.

Presence of a latent mitochondrial targeting signal in gene on mitochondrial genome

Ueda, M., Fujimoto, M., Arimura, S.-i., Tsutsumi, N., Kadowaki, K.-i. — 2008-06-23

^{Organelles, such as mitochondria and chloroplasts, are derived from endosymbionts. Gene transfer events from organelles to the nucleus have occurred over evolutionary time. In the case that a transferred gene in the nucleus needs to go back to the original organelle, it must obtain targeting information for sorting its protein to that organelle. Here, we reveal that the genes for the ribosomal proteins L2 and S4 in the Arabidopsis thaliana mitochondrial (mt) genome contain information for protein targeting into the mitochondria. Similarly, the genes for the ribosomal proteins L2 and S19 in the Oryza sativa mt genome contain information for protein targeting into mitochondria. These results suggest that targeting information already existed in each gene in the plant mt genome before the transfer event to the nucleus occurred. We provide new insights into the timing of the appearance of targeting signals in evolution.}

Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast

2008-06-23

The yeast Saccharomyces cerevisiae proliferates rapidly in glucose-containing media. As glucose is getting depleted, yeast cells enter the transition from fermentative to non-fermentative metabolism, known as the diauxic shift, which is associated with major changes in gene expression. To understand the expression evolution of genes involved in the diauxic shift and in non-fermentative metabolism within species, a laboratory strain (BY), a wild strain (RM), and a clinical isolate (YJM) were used in this study. Our data showed that the RM strain enters into the diauxic shift ~1 hour earlier than the BY strain with an earlier, higher induction of many key transcription factors (TFs) involved in the diauxic shift. Our sequence data revealed sequence variations between BY and RM in both coding and promoter regions of the majority of these TFs. The key TF Cat8p, a zinc-finger cluster protein, is required for the expression of many genes in gluconeogenesis under non-fermentative growth and its derepression is mediated by deactivation of Mig1p. Our kinetic study of CAT8 expression revealed that CAT8 induction corresponded to the timing of glucose depletion in both BY and RM and CAT8 was induced up to 50-90 folds in RM, whereas only 20-30 folds in BY. In order to decipher the relative importance of cis- and trans-variations in expression divergence in the gluconeogenic pathway during the diauxic shift, we studied the expression levels of MIG1, CAT8, and their downstream target genes in the co-cultures and in the hybrid diploids of BY-RM, BY-YJM, and RM-YJM, and in strains with swapped promoters. Our data showed that the differences between BY and RM in the expression of MIG1, the upstream regulator of CAT8, were affected mainly by changes in cis elements, though also by changes in trans-acting factors, whereas those of CAT8 and its downstream target genes were predominantly affected by changes in trans-acting factors.

Interacting Gene Clusters and the Evolution of the Vertebrate Immune System

Makino, T., McLysaght, A. — 2008-06-23

Unravelling the "code" of genome structure is an important goal of genomics research. Co-localization of genes in eukaryotic genomes may facilitate preservation of favourable allele combinations between epistasic loci or co-regulation of functionally-related genes. However, the presence of interacting gene clusters in the human genome has remained unclear. We systematically searched the human genome for evidence of closely-linked genes whose protein products interact. We find 83 pairs of interacting genes that are located within 1 Mbp on the human genome, or 37 if we exclude hub proteins. This number of interacting gene clusters is significantly more than expected by chance, and is not the result of tandem duplications. Furthermore, we find that these clusters are significantly more conserved across vertebrate (but not chordate) genomes than other pairs of genes located within 1 Mbp in the human genome. In many cases the genes are both present but not clustered in older vertebrate lineages. These results suggest gene cluster creation along the human lineage. These clusters are not enriched for housekeeping genes, but we find a significant contribution from genes involved in "response to stimulus". Many of these genes are involved in the immune response, including, but not limited to, known clusters such as the MHC. That these clusters were formed contemporaneously with the origin of adaptive immunity within the vertebrate lineage suggests that novel evolutionary and regulatory constraints were associated with the operation of the immune system.

Arthropod 7SK RNA

2008-06-19

The 7SK snRNA is a key player in the regulation of polymerase II transcription. 7SK RNA was long believed to be specific to vertebrates where it is highly conserved. Homologs in basal deuterostomes and a few lophotrochozoan species were only recently reported. On longer time scales 7SK evolves rapidly with only few conserved sequence and structure motifs. Previous attempts to identify the Drosophila homolog thus have remained unsuccessful despite considerable efforts. Here we report on the discovery of arthropod 7SK RNAs using a novel search strategy based on polymerase III promoters, as well as the subsequent verification of its expression. Our results demonstrate that a 7SK snRNA featuring two highly structured conserved domains was present already in the bilaterian ancestor.

Evolution of closely linked gene pairs in vertebrate genomes

Franck, E., Hulsen, T., Huynen, M. A., de Jong, W. W., Lubsen, N. H., Madsen, O. — 2008-06-19

The orientation of closely linked genes in mammalian genomes is not random: there are more head-to-head (h2h) gene pairs than expected. To understand the origin of this enrichment in h2h gene pairs, we have analyzed the phylogenetic distribution of gene pairs separated by less than 600 bp of intergenic DNA ("gene duos"). We show here that a lack of head-to-tail (h2t) gene duos is an even more distinctive characteristic of mammalian genomes, with the platypus genome as the only exception. In non-mammalian vertebrate and in non-vertebrate genomes the frequency of h2h, h2t and tail-to-tail (t2t) gene duos is close to random. In tetrapod genomes the h2t and t2t gene duos are more likely to be part of a larger gene cluster of closely spaced genes than h2h gene duos; in fish and urochordate genomes the reverse is seen. In human and mouse tissues the expression profiles of gene duos were skewed toward positive co-expression, irrespective of orientation. The organization of orthologs of both members of about 40% of the human gene duos could be traced in other species, enabling a prediction of the organization at the branch points of gnathostomes, tetrapods, amniotes and euarchontoglires. The accumulation of h2h gene duos started in tetrapods, while that of h2t and t2t gene duos only started in amniotes. The apparent lack of evolutionary conservation of h2t and t2t gene duos relative to that of h2h gene duos is thus a result of their relatively late origin in the lineage leading to mammals; we show that once they are formed h2t and t2t gene duos are as stable as h2h gene duos.

Similar numbers but different repertoires of olfactory receptor genes in humans and chimpanzees

Go, Y., Niimura, Y. — 2008-06-17

Animals recognize their external world through the detection of tens of thousands of chemical odorants. Olfactory receptor (OR) genes encode proteins for detecting odorant molecules and form the largest multigene family in mammals. It is known that humans have fewer OR genes and a higher fraction of OR pseudogenes than mice or dogs. To investigate whether these features are human-specific or common to all higher primates, we identified nearly complete sets of OR genes from the chimpanzee and macaque genomes and compared them with the human OR genes. In contrast to previous studies, here we show that the number of OR genes (~810) and the fraction of pseudogenes (51%) in chimpanzees are very similar to those in humans, though macaques have considerably fewer OR genes. The pseudogenization rates and the numbers of genes affected by positive selection are also similar between humans and chimpanzees. Moreover, the most recent common ancestor between humans and chimpanzees had a larger number of functional OR genes (>500) and a lower fraction of pseudogenes (41%) than its descendents, suggesting that the OR gene repertoires are in a phase of deterioration in both lineages. Interestingly, despite the close evolutionary relationship between the two species, approximately 25% of their functional gene repertoires are species-specific due to massive gene losses. These findings suggest that the tempo of evolution of OR genes is similar between humans and chimpanzees, but the OR gene repertoires are quite different between them. This difference might be responsible for the species-specific ability of odor perception.

Intense transpositional activity of insertion sequences in an ancient obligate endosymbiont

2008-06-17

The streamlined genomes of ancient obligate endosymbionts generally lack transposable elements, such as insertion sequence (IS). Yet, the genome of Wolbachia, one of the most abundant bacterial endosymbionts on Earth, is littered with IS. Such a paradox raises the question as to why there are so many IS in the genome of this ancient endosymbiont. To address this question, we investigated IS transpositional activity in the unculturable Wolbachia by tracking the evolutionary dynamics and history of ISWpi1 elements. We show that: (i) ISWpi1 is widespread in Wolbachia, being present in at least 55% of the 40 sampled strains, (ii) ISWpi1 copies exhibit virtually identical nucleotide sequences both within and among Wolbachia genomes and possess an intact transposase gene, (iii) individual ISWpi1 copies are differentially inserted among Wolbachia genomes, and (iv) ISWpi1 occurs at variable copy numbers among Wolbachia genomes. Collectively, our results provide compelling evidence for intense ISWpi1 transpositional activity and frequent ISWpi1 horizontal transmission among strains during recent Wolbachia evolution. Thus, the genomes of ancient obligate endosymbionts can carry high loads of functional and transpositionally active transposable elements. Our results also indicate that Wolbachia genomes have experienced multiple and temporally distinct ISWpi1 invasions during their evolutionary history. Such recurrent exposition to new IS invasions may explain, at least partly, the unusually high density of transposable elements found in the genomes of Wolbachia endosymbionts.

Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group

2008-06-12

The obligate intracellular bacterium Wolbachia pipientis strain wPip induces cytoplasmic incompatibility (CI), patterns of crossing sterility, in the Culex pipiens group of mosquitoes. The complete sequence is presented of the 1.48 Mbp genome of wPip which encodes 1386 CDS, representing the first genome sequence of a B-supergroup Wolbachia. Comparisons were made with the smaller genomes of Wolbachia strains wMel of Drosophila melanogaster, an A-supergroup Wolbachia that is also a CI-inducer, and wBm, a mutualist of Brugia malayi nematodes that belongs to the D-supergroup of Wolbachia. Despite extensive gene order re-arrangement, a core set of Wolbachia genes shared between the three genomes can be identified and contrasts with a flexible gene pool where rapid evolution has taken place. There are much more extensive prophage and ankyrin repeat encoding (ANK) gene components of the wPip genome compared to wMel and wBm, and both are likely to be of considerable importance in wPip biology. Five WO-B-like prophage regions are present and contain some genes that are identical or highly similar in multiple prophage copies, while other genes are unique, and it is likely that extensive recombination, duplication and insertion has occurred between copies. A much larger number of genes encode ankyrin repeat (ANK) proteins in wPip, with 60 present compared to 23 in wMel, many of which are within or close to the prophage regions. It is likely that this pattern is partly a result of expansions in the wPip lineage, due for example to gene duplication, but their presence is in some cases more ancient. The wPip genome underlines the considerable evolutionary flexibility of Wolbachia, providing clear evidence for the rapid evolution of ANK-encoding genes and of prophage regions. This host-Wolbachia system, with its complex patterns of sterility induced between populations, now provides an excellent model for unravelling the molecular systems underlying host reproductive manipulation.

Neutrality of foreign complex subunits in an experimental model of lateral gene transfer

Wellner, A., Gophna, U. — 2008-06-12

Lateral gene transfer is a powerful force in microbial evolution. However, the barriers that restrict this evolutionary phenomenon are not fully understood. It has long been observed that genes that encode subunits of complexes exhibit relatively compatible phylogenies, implying mostly vertical evolution. This may be explained by the failure of a new gene product to effectively interact with pre-existing protein subunits, making its acquisition neutral – a theory termed the "complexity hypothesis". On the other hand, such genes may reduce the fitness of the host by disturbing the stoichiometric balance between complex subunits, resulting in purifying selection against gene retention. To examine these two alternative scenarios we designed an experimental system that mimics the transfer of genes encoding homologs of essential complex subunits into the model bacterium Escherichia coli. In addition, we over-expressed the native E. coli gene in order to examine the contribution of gene dosage effects. We show that accumulation of native or foreign complex subunits in the cell does not result in loss of fitness, except for a minor fitness reduction observed for a single foreign homolog. Indeed, a series of genetic and biochemical assays failed to detect any interaction between the foreign subunits and the native polypeptides of the complex, implying an inability of such transfer events to generate positive selection for gene retention. We conclude that lateral gene transfer of complex subunits may be mostly neutral and that forces operating against gene retention appear to be moderate.

Compensatory evolution in RNA secondary structures increases substitution rate variation among sites

2008-06-04

There is growing evidence that interactions between biological molecules (e.g. RNA-RNA, protein-protein, RNA-protein) place limits on the rate and trajectory of molecular evolution. Here, by extending Kimura's (1985) model of compensatory evolution at interacting sites, we show that the ratio of transition to transversion substitutions () at interacting sites should be equal to the square of the ratio at independent sites. Since transition mutations generally occur at a higher rate than transversions, the model predicts that should be higher at interacting sites than at independent sites. We tested this prediction in ten RNA secondary structures by comparing phylogenetically-derived estimates of in paired sites within stems (_p) and unpaired sites within loops (_u). Eight of the ten structures showed an excellent match to the quantitative predictions of the model, and nine of the ten structures matched the qualitative prediction _p > _u. Only the rev response element (RRE) from the HIV genome showed the reverse pattern, with _p < _u. Although a variety of evolutionary forces could produce quantitative deviations from the model predictions, the reversal in magnitude of _p and _u could by achieved only by violating the model assumption that the underlying transition (or transversion) mutation rates were identical in paired and unpaired regions of the molecule. We explore the ability of the APOBEC3 enzymes, host defense mechanisms against retroviruses, that induce transition mutations preferentially in single-stranded regions of the HIV genome, to explain this exception to the rule. Taken as a whole, our findings suggest that may have utility as a simple diagnostic to evaluate proposed secondary structures.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germline

Zhao, Y., Epstein, R. J. — 2008-06-04

Tumor suppressor genes are classified by their somatic behavior either as caretakers (CTs) that maintain DNA fidelity or as gatekeepers (GKs) that regulate cell survival, but the germline role of these disease-related gene subgroups may differ. To test this hypothesis, we have used genomic data mining to compare the features of human CTs (n = 38), GKs (n = 36), DNA repair genes (n = 165), apoptosis genes (n = 622), and their orthologs. This analysis reveals that repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms (p < 0.01), whereas CT orthologs are commoner than GK orthologs in unicellular organisms (p < 0.05). Gene targeting data show that CTs are less essential than GKs for survival of multicellular organisms (p < 0.0005), and that CT knockouts often permit offspring viability at the cost of male sterility. Patterns of human familial oncogenic mutations confirm that isolated CT loss is commoner than is isolated GK loss (p < 0.00001). In sexually reproducing species CTs appear subject to less efficient purifying selection (i.e., higher Ka/Ks) than GKs (p = 0.000003); the faster evolution of CTs seems likely to be mediated by gene methylation and reduced transcription-coupled repair, based on differences in dinucleotide patterns (p = 0.001). These data suggest that germline CT/repair gene function is relatively dispensable for survival, and imply that milder (e.g., epimutational) male pre-zygotic repair defects could enhance sperm variation – and hence environmental adaptation and speciation – while sparing fertility. We submit that CTs and repair genes are general targets for epigenetically-initiated adaptive evolution, and propose a model in which human cancers arise in part as an evolutionarily programmed side-effect of age- and damage-inducible genetic instability affecting both somatic and germline lineages.

Frequent, phylogenetically local horizontal transfer of the cox1 group I intron in flowering plant mitochondria

Sanchez-Puerta, M. V., Cho, Y., Mower, J. P., Alverson, A. J., Palmer, J. D. — 2008-06-03

Horizontal gene transfer is surprisingly common among plant mitochondrial genomes. The first well-established case involves a homing group I intron in the mitochondrial cox1 gene shown to have been frequently acquired via horizontal transfer in angiosperms. Here we report extensive additional sampling of angiosperms, including 85 newly sequenced introns from 30 families. Analysis of all available data leads us to conclude that, among the 640 angiosperms (from 212 families) whose cox1 intron status has been characterized thus far, the intron has been acquired via roughly 70 separate horizontal transfer events. We propose that the intron was originally seeded into angiosperms by a single transfer from fungi, with all subsequent inferred transfers occurring from one angiosperm to another. The pattern of angiosperm-to-angiosperm transfer is biased towards exchanges between plants belonging to the same family. Illegitimate pollination is proposed as one potential factor responsible for this pattern, given that aberrant, cross-species pollination is more likely between close relatives. Other potential factors include shared vectoring agents or common geographic locations. We report the first apparent cases of loss of the cox1 intron; losses are accompanied by retention of the exonic coconversion tract, which is located immediately downstream of the intron and which is a product of the intron's self-insertion mechanism. We discuss the many reasons why the cox1 intron is so frequently and detectably transferred, and rarely lost, and conclude that it should be regarded as the "canary in the coal mine" with respect to horizontal transfer in angiosperm mitochondria.

Gene Flow and Natural Selection in Oceanic Human Populations, Inferred from Genome-wide SNP Typing

2008-06-03

It is suggested that the major prehistoric human colonizations of Oceania occurred twice, namely, about 50,000 and 4,000 years ago. The first settlers are considered as ancestors of indigenous people in New Guinea and Australia. The second settlers are Austronesian-speaking people who dispersed by voyaging in the Pacific Ocean. In this study, we performed genome-wide SNP typing on an indigenous Melanesian (Papuan) population, Gidra, and a Polynesian population, Tongans, by using the Affymetrix 500K assay. The SNP data were analyzed together with the data of the HapMap samples provided by Affymetrix. In agreement with previous studies, our phylogenetic analysis indicated that indigenous Melanesians are genetically closer to Asians than to Africans and European Americans. Population structure analyses revealed that the Tongan population is genetically originated from Asians at 70% and indigenous Melanesians at 30%, which thus supports the so-called "Slow train" model. We also applied the SNP data to genome-wide scans for positive selection by examining haplotypic variation, and identified many candidates of locally selected genes. Providing a clue to understand human adaptation to environments, our approach based on evolutionary genetics must contribute to revealing unknown gene functions as well as functional differences between alleles. Conversely, this approach can also shed some light onto the invisible phenotypic differences between populations.

Inferring Natural Selection on Fine-Scale Chromatin Organization in Yeast

Babbitt, G.A., Kim, Y. — 2008-05-29

Despite its potential role in the evolution of complex phenotypes, the detection of negative (purifying) and positive selection on non-coding regulatory sequence has been elusive because of the inherent difficulty in predicting the functional consequences of mutations on non-coding sequence. Because the functioning of regulatory sequence depends upon both chromatin configuration and cis-regulatory factor binding, we investigate the idea that the functional conservation of regulatory regions should be associated with the conservation of sequence-dependent bending properties of DNA that determine its affinity for the nucleosome. Recent advances in the computational prediction of sequence-dependent affinity to nucleosomes provide an opportunity to distinguish between neutral and non-neutral evolution of fine-scale chromatin organization. Here, a statistical test is presented for detecting evolutionary conservation and/or adaptive evolution of nucleosome affinity from interspecies comparisons of DNA sequences. Local nucleosome affinities of homologous sequences were calculated using two recently published methods. A randomization test was applied to sites of mutation to evaluate the similarity of DNA-nucleosome affinity between several closely related species of Saccharomyces yeast. For most of the genes we analyzed, the conservation of local nucleosome affinity was detected at a few distinct locations in the upstream non-coding region. Our results also demonstrate that different patterns of chromatin evolution have shaped DNA-nucleosome interaction in at the core promoters of TATA-containing and TATA-less genes, and that elevated purifying selection has maintained low affinity for nucleosome in the core promoters of the latter group. Across the entire yeast genome, DNA-nucleosome interaction was also discovered to be significantly more conserved in TATA-less genes compared to TATA-containing genes.

Positive and negative selection on noncoding DNA in Drosophila simulans

Haddrill, P. R., Bachtrog, D., Andolfatto, P. — 2008-05-29

There is now a wealth of evidence that some of the most important regions of the genome are found outside those that encode proteins, and noncoding regions of the genome have been shown to be subject to substantial levels of selective constraint, particularly in Drosophila. Recent work has suggested that these regions may also have been subject to the action of positive selection, with large fractions of noncoding divergence having been driven to fixation by adaptive evolution. However, this work has focussed on Drosophila melanogaster, which is thought to have experienced a reduction in effective population size (N_e), and thus a reduction in the efficacy of selection, compared to its closest relative Drosophila simulans. Here, we examine patterns of evolution at several classes of noncoding DNA in D. simulans, and find that all noncoding DNA is subject to the action of negative selection, indicated by reduced levels of polymorphism and divergence, and a skew in the frequency spectrum towards rare variants. We find that the signature of negative selection on noncoding DNA and nonsynonymous sites is obscured to some extent by purifying selection acting on preferred to unpreferred synonymous codon mutations. We investigate the extent to which divergence in noncoding DNA is inferred to be the product of positive selection and to what extent these inferences depend on selection on synonymous sites and demography. Based on patterns of polymorphism and divergence for different classes of synonymous substitution, we find the divergence excess inferred in noncoding DNA and nonsynonymous sites in the D. simulans lineage difficult to reconcile with demographic explanations.

A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus

Kosakovsky Pond, S. L., Poon, A. F.Y., Leigh Brown, A. J., Frost, S. D.W. — 2008-05-29

We develop a model-based phylogenetic maximum likelihood test for evidence of preferential substitution towards a given residue at individual positions of a protein alignment – Directional Evolution of Protein Sequences (DEPS). DEPS can identify both the target residue and sites evolving towards it, help detect selective sweeps and frequency dependent selection – scenarios that confound most existing tests for selection, and achieves good power and accuracy on simulated data. We applied DEPS to alignments representing different genomic regions of Influenza A virus (IAV), sampled from avian hosts (H5N1 serotype) and human hosts (H3N2 serotype) and identified multiple directionally evolving sites in 5/8 genomic segments of H5N1 and H3N2 IAV. We propose a simple descriptive classification of directionally evolving sites into 5 groups based on the temporal distribution of residue frequencies, and document known functional correlates, such as immune escape or host adaptation.

The Impact of Founder Events on Chromosomal Variability in Multiply Mating Species

Pool, J. E., Nielsen, R. — 2008-05-28

In species with heterogametic males, the relative levels of X chromosome versus autosome diversity hold key information about the evolutionary forces at work in a population. It has been shown that population size changes alter the ratio of X-linked to autosomal (X/A) variation, with population size reductions and recent bottlenecks leading to decreased X/A diversity ratios. Here we use theory and simulation to investigate a separate demographic effect - that of founder events involving multiply mated females - and find that it leads to much stronger reductions in X/A diversity ratios than are produced by simple population size changes. Investigating the potential of this process to account for sharply reduced X-linked diversity in European Drosophila melanogaster, we find that this model yields predictions that are compatible with the empirical data.

Natural selection against protein aggregation on self-interacting and essential proteins in yeast, fly and worm

Chen, Y., Dokholyan, N. V. — 2008-05-23

Protein aggregation is the phenomenon of protein self-association potentially leading to detrimental effects on physiology, which is closely-related to numerous human diseases such as Alzheimer's and Parkinson's disease. Despite progress in understanding the mechanism of protein aggregation, how natural selection against protein aggregation acts on subunits of protein complexes and on proteins with different contributions to organism fitness remains largely unknown. Here, we perform a proteome-wide analysis by using an experimentally-validated algorithm TANGO and utilizing sequence, interactomic and phenotype-based functional genomic data from yeast, fly and nematode. We find that proteins that are capable of forming homo-oligomeric complex have lower aggregation propensity compared with proteins that do not function as homo-oligomer. Further, proteins that are essential to the fitness of an organism have lower aggregation propensity compared with non-essential ones. Our finding suggests that the selection force against protein aggregation acts across different hierarchies of biological system.

The sperm proteins from amphioxus mirror its basal position among chordates and redefine the origin of vertebrate protamines

Eirin-Lopez, J. M., Frehlick, L. J., Chiva, M., Saperas, N., Ausio, J. — 2008-05-23

The sperm nuclear basic proteins (SNBPs) that participate in chromatin condensation in spermatozoa belong to three groups: histone (H), protamine-like (PL) and protamine type. They share a common origin with histone H1 resulting from the segregation of PL components, corresponding to different regions of an H1 precursor molecule (N-terminal, winged-helix domain, C-terminal), becoming independent and following a subsequent process of parallel vertical evolution (H PL P). In the present work we describe the sequence and primary structure of the main SNBP component in the sperm of the cephalochordate Branchiostoma floridae (amphioxus), revealing that it represents the deuterostome counterpart of the PL-III SNBP component from molluscs corresponding to the H1 N-terminal region. Until now, this has been a missing piece needed to complete the evolutionary history of SNBPs in metazoan genomes. The discovery of this PL lineage in deuterostomes definitively validates the parallel vertical evolution of SNBPs across metazoans, giving further support to the ‘basal’ position of amphioxus among chordates, with respect to tunicates. Sequence analyses suggest that later on in evolution the appearance of positively selected arginine-rich protamines, derived from the H1 C-terminal region, led to the extinction of this PL lineage in the genomes of early protostomes and deuterostomes. Given that tunicates are now viewed as a sister group of vertebrates, the lysine to arginine transition responsible for the origin of vertebrate protamines must be set a step back from tunicates.

Non-Toxic Strains of Cyanobacteria are the Result of Major Gene Deletion Events Induced by a Transposable Element

Christiansen, G., Molitor, C., Philmus, B., Kurmayer, R. — 2008-05-22

Blooms that are formed by cyanobacteria consist of toxic and non-toxic strains. The mechanisms that result in the occurrence of non-toxic strains are enigmatic. All of the non-toxic strains of the filamentous cyanobacterium Planktothrix that were isolated from nine European countries were found to have lost 90% of a large gene cluster (mcy) that encoded the synthesis of the toxic peptide microcystin. Those strains still contain the flanking regions of the mcy gene cluster along with remnants of the transposable elements that are found in between. The majority of the strains still contain a gene coding for a distinct thioesterase type II (mcyT), which is putatively involved in microcystin synthesis. The insertional inactivation of mcyT in a microcystin-producing strain resulted in the reduction of microcystin synthesis by 94±2% (1 SD). Non-toxic strains that occur in shallow lakes throughout Europe form a monophyletic lineage. A second lineage consists of strains that contain the mcy gene cluster but differ in their photosynthetic pigment composition, which is due to the occurrence of strains that contain phycocyanin or large amounts of phycoerythrin in addition to phycocyanin. Strains containing phycoerythrin typically occur in deep-stratified lakes. The rare occurrence of gene cluster deletion, paired with the evolutionary diversification of the lineages of strains that lost or still contain the mcy gene cluster, needs to be invoked in order to explain the absence or dominance of toxic cyanobacteria in various habitats.

Spatial and temporal heterogeneity in nucleotide sequence evolution

Whelan, S. — 2008-05-22

Models of nucleotide substitution make many simplifying assumptions about the evolutionary process, including that the same process acts on all sites in an alignment and on all branches on the phylogenetic tree. Many studies have shown that in reality the substitution process is heterogeneous and that this variability can introduce systematic errors into many forms of phylogenetic analyses. I propose a new rigorous approach for describing heterogeneity called a temporal hidden Markov model (THMM), which can distinguish between among site (spatial) heterogeneity and among lineage (temporal) heterogeneity. Several versions of the THMM are applied to 16 sets of aligned sequences to quantitatively assess the different forms of heterogeneity acting within them. The most general THMM provides the best fit in all of the data sets examined, providing strong evidence of pervasive heterogeneity during evolution. Investigating individual forms of heterogeneity provides further insights. In agreement with previous studies, spatial rate heterogeneity (rates across sites: RAS) is inferred to be the single most prevalent form of heterogeneity. Interestingly, RAS appears so dominant that failure to independently include it in the THMM masks other forms of heterogeneity, particularly temporal heterogeneity. Incorporating RAS into the THMM reveals substantial temporal and spatial heterogeneity in nucleotide composition and bias towards transition substitution in all alignments examined, although the relative importance of different forms of heterogeneity varies between data sets. Furthermore, the improvements in model fit observed by adding complexity to the model suggest that the THMMs used in this study do not capture all the evolutionary heterogeneity occurring in the data. These observations all indicate that current tests may consistently underestimate the degree of temporal heterogeneity occurring in data. Finally, there is a weak link between the amount of heterogeneity detected and the level of divergence between the sequences, suggesting that variability in the evolutionary process will be a particular problem for deep phylogeny.

Reconstructing Evolutionary Graphs: 3D Parsimony

Lake, J. A. — 2008-05-19

The increasing recognition that symbioses have greatly altered evolution through genome fusions is creating a need for algorithms that can reliably detect and reconstruct fusions. Here we generalize the bootstrappers gambit algorithm (a quartet method) in order to permit it to analyze both bifurcations and fusions under a single mathematical model, and thereby detect past genomic branchings and endosymbioses. This new method, 3D parsimony, can be applied to aligned sequences, such as gene-, indel-, or other genomic presence/absence sequences. It also provides a statistical measure of support for each possible graph. The usefulness of this method is demonstrated by applying it to the Ring of Life.

Widespread ultraconservation divergence in primates

Ovcharenko, I. — 2008-05-19

The distribution and evolution of ultraconserved elements (UCEs, DNA stretches that are perfectly identical in primates and rodents) were examined in genomes of three primate species (human, chimpanzee, and rhesus macaque). It was found that the number of UCEs has decreased throughout primate evolution. At least 26% of ancestral UCEs have diverged in hominoids, while an additional 17% have accumulated one or more single nucleotide polymorphisms (SNPs) in the human genome. Sequence polymorphism analyses indicate that mutation fixation within an UCE can trigger a relaxation in the selective constraint on that element. Homogeneous mutation accumulations in UCEs served as a template by which purifying selection acted more effectively on protein-coding UCEs. Gene ontology annotation suggests that UCE sequence variation, primarily occurring in noncoding regions, might be linked to the reprogramming of the expression pattern of transcription factors and developmentally important genes. Many of these genes are expressed in the central nervous system. Finally, UCE sequence variability within human populations has been identified, including population-specific non-synonymous changes in protein-coding regions.

Signature Genes as a Phylogenomic Tool

Dutilh, B. E., Snel, B., Ettema, T. J.G., Huynen, M. A. — 2008-05-19

Gene content has been shown to contain a strong phylogenetic signal, yet its usage for phylogenetic questions is hampered by horizontal gene transfer and parallel gene loss, and until now required completely sequenced genomes. Here, we introduce an approach that allows the phylogenetic signal in gene content to be applied to any set of sequences, using signature genes for phylogenetic classification. The hundreds of publicly available genomes allow us to identify signature genes at various taxonomic depths, and we show how the presence of signature genes in an unspecified sample can be used to characterize its taxonomic composition.

We identify 8,362 signature genes specific for 112 prokaryotic taxa. We show that these signature genes can be used to address phylogenetic questions on the basis of gene content in cases where classic gene content or sequence analyses provide an ambiguous answer, such as for Nanoarchaeum equitans, and even in cases where complete genomes are not available, such as for metagenomics data. Cross-validation experiments leaving out up to 30% of the species show that ~92% of the signature genes correctly place the species in a related clade. Analyses of metagenomics data sets with the signature gene approach are in good agreement with the previously reported species distributions based on phylogenetic analysis of marker genes. Summarising, signature genes can complement traditional sequence based methods in addressing taxonomic questions.

Mitochondrial DNA phylogeny in Eastern and Western Slavs

2008-05-13

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 (~ 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.

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

Elias, M. — 2008-05-13

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.

Overdispersion Of The Molecular Clock: Temporal Variation Of Gene-Specific Substitution Rates In Drosophila

Bedford, T., Hartl, D. L. — 2008-05-13

Simple models of molecular evolution assume that sequences evolve by a Poisson process in which nucleotide or amino acid substitutions occur as rare independent events. In these models the expected ratio of the variance to the mean of substitution counts equals 1, and substitution processes with a ratio greater than 1 are called overdispersed. Comparing the genomes of 10 closely related species of Drosophila, we extend earlier evidence for overdispersion in amino acid replacements as well as in four-fold synonymous substitutions. The observed deviation from the Poisson expectation can be described as a linear function of the rate at which substitutions occur on a phylogeny, which implies that deviations from the Poisson expectation arise from gene-specific temporal variation in substitution rates. Amino acid sequences show greater temporal variation in substitution rates than do four-fold synonymous sequences. Our findings provide a general phenomenological framework for understanding overdispersion in the molecular clock. Also, the presence of substantial variation in gene-specific substitution rates has broad implications for work in phylogeny reconstruction and evolutionary rate estimation.

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

Baines, J. F., Sawyer, S. A., Hartl, D. L., Parsch, J. — 2008-05-13

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.

DNA METHYLATION AND STRUCTURAL AND FUNCTIONAL BIMODALITY OF VERTEBRATE PROMOTERS

Elango, N., Yi, S. V. — 2008-05-09

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.

Convergent evolution of clustering of Iroquois homeobox genes across metazoans

Irimia, M., Maeso, I., Garcia-Fernandez, J. — 2008-05-09

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.

The deep archaeal roots of eukaryotes

Yutin, N., Makarova, K. S., Mekhedov, S. L., Wolf, Y. I., Koonin, E. V. — 2008-05-06

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.

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

Grus, W. E., Zhang, J. — 2008-05-05

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.

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

Ferguson, W., Dvora, S., Gallo, J., Orth, A., Boissinot, S. — 2008-05-05

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.

How well does the HoT score reflect sequence alignment accuracy?

Hall, B. G. — 2008-05-04

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.

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

Xie, Z., Li, X., Glover, B. J., Bai, S., Rao, G.-Y., Luo, J., Yang, J. — 2008-05-02

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.

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

Prasad, A. B., Allard, M. W., NISC Comparative Sequencing Program, Green, E. D. — 2008-05-02

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.

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

2008-05-02

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.

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

Liao, B.-Y., Zhang, J. — 2008-04-24

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.

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

Nobrega, C., Kahdem, M., Aguade, M., Segarra, C. — 2008-04-23

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 O₃ inversion, a moderately-sized inversion at Muller's element E. Indeed, a strong genetic differentiation all over O₃ 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 A₂ inversion was analyzed in A_st and A₂ chromosomes of D. subobscura. A₂ is a medium-sized inversion at Muller's element A and forms a single inversion loop in heterokaryotypes. The lower level of variation in A₂ relative to A_st and the significant excess of low frequency variants at polymorphic sites indicate that nucleotide variation at A₂ 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 A₂ and A_st chromosomes than P236, as revealed by F_ST and LD estimates. However, significant genetic differentiation between the A_st and A₂ 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 A₂ inversion. A₂ 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.

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

Martin, V., Domingo, E. — 2008-04-23

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.

Insights into the Evolution of the Motilin/Ghrelin-Associated Family and Their Receptors

He, J., Irwin, D. M., Zhang, Y.-p. — 2007-09-28

This article was published in error and has been removed.