New evolutionary frontiers from unusual virus genomes

The sequences of two giant viral genomes, Mimivirus and a polydnavirus, have recently been published. Mimivirus has the largest known viral genome and encodes an unprecedented number of proteins, whereas the polydnavirus genome has an extremely low coding density and does not encode DNA-replication proteins. These and other unusual features challenge the way we view the evolution and definition of viruses

Systematics of Diparinae (Hymenoptera: Pteromalidae), and their position within the broader context of pteromalid phylogeny

Chalcidoidea, one of the largest superfamilies of parasitic Hymenoptera, has major importance in the biological control of insect pests. However, phylogenetic relationships both within and between chalcidoid families have been poorly understood, particularly within Pteromalidae, one of largest families. This study approaches the problem of pteromalid phylogeny from two directions, coupling a detailed morphological revision of one of the most divergent and poorly-known subfamilies of pteromalids (Diparinae) with a broad, exemplar-based molecular study that seeks to place this subfamily in the broader context of pteromalid and chalcidoid phylogeny. First, a morphological phylogenetic analysis of the world genera of Diparinae is provided based on 76 characters. Diparinae is supported as monophyletic based on the presence of a cercal brush in all analyses. The cercal brush, in combination with the absence of a smooth, convex dorsellum, is diagnostic for Diparinae. Liepara Boucek (Pteromalidae) and Bohpa Darling (Pteromalidae: Ceinae) both appear as sister-groups to Diparinae in different analyses. The phylogenetic analysis is used to develop a new classification scheme, under which Diparinae consists of 116 species in 14 genera. Three genera and 14 species are described as new, and a key to all genera is provided. Second, forty-two taxa broadly representing Chalcidoidea and more specifically Pteromalidae were sequenced for 4620 bp of four nuclear protein-coding genes, including 1719bp of CAD, 708bp of DDC, 1142bp of enolase, and 1044bp of PEPCK. The combined data set was analyzed using maximum likelihood methods, and the AU test was used to test support for non-monophyly of taxonomic groups which appeared para- or poly-phyletic in the tree. Phylogenetic relationships that have been supported by previous morphological and molecular evidence were recovered (e.g., monophyly of Chalcidoidea), as was the monophyly of groups well supported by morphology but resolved as polyphyletic in previous molecular analyses (e.g., Chalcididae). The monophyly of Pteromalidae and the pteromalid subfamily Colotrechninae are both strongly rejected (p<0.001). New hypotheses are proposed for relationships within Chalcidoidea, including Eutrichosomatinae (Pteromalidae) as the basal lineage of the perilampid/eucharitid clade. This study demostrates that molecular and morphological data can provide reciprocal illumination for understanding relationships within Chalcidoidea

Accelerated microevolution in an outer membrane protein (OMP) of the intracellular bacteria Wolbachia

<p>Abstract</p> <p>Background</p> <p>Outer membrane proteins (OMPs) of Gram-negative bacteria are key players in the biology of bacterial-host interactions. However, while considerable attention has been given to OMPs of vertebrate pathogens, relatively little is known about the role of these proteins in bacteria that primarily infect invertebrates. One such OMP is found in the intracellular bacteria <it>Wolbachia</it>, which are widespread symbionts of arthropods and filarial nematodes. Recent experimental studies have shown that the <it>Wolbachia </it>surface protein (WSP) can trigger host immune responses and control cell death programming in humans, suggesting a key role of WSP for establishment and persistence of the symbiosis in arthropods.</p> <p>Results</p> <p>Here we performed an analysis of 515 unique alleles found in 831 <it>Wolbachia </it>isolates, to investigate WSP structure, microevolution and population genetics. WSP shows an eight-strand transmembrane β-barrel structure with four extracellular loops containing hypervariable regions (HVRs). A clustering approach based upon patterns of HVR haplotype diversity was used to group similar WSP sequences and to estimate the relative contribution of mutation and recombination during early stages of protein divergence. Results indicate that although point mutations generate most of the new protein haplotypes, recombination is a predominant force triggering diversity since the very first steps of protein evolution, causing at least 50% of the total amino acid variation observed in recently diverged proteins. Analysis of synonymous variants indicates that individual WSP protein types are subject to a very rapid turnover and that HVRs can accommodate a virtually unlimited repertoire of peptides. Overall distribution of WSP across hosts supports a non-random association of WSP with the host genus, although extensive horizontal transfer has occurred also in recent times.</p> <p>Conclusions</p> <p>In OMPs of vertebrate pathogens, large recombination impact, positive selection, reduced structural and compositional constraints, and extensive lateral gene transfer are considered hallmarks of evolution in response to the adaptive immune system. However, <it>Wolbachia </it>do not infect vertebrates. Here we predict that the rapid turnover of WSP loop motifs could aid in evading or inhibiting the invertebrate innate immune response. Overall, these features identify WSP as a strong candidate for future studies of host-<it>Wolbachia </it>interactions that affect establishment and persistence of this widespread endosymbiosis.</p

Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia

Homologous meiotic recombination occurs in most sexually reproducing organisms, yet its evolutionary advantages are elusive. Previous research explored recombination in the honeybee, a eusocial hymenopteran with an exceptionally high genome-wide recombination rate. A comparable study in a non-social member of the Hymenoptera that would disentangle the impact of sociality from Hymenoptera-specific features such as haplodiploidy on the evolution of the high genome-wide recombination rate in social Hymenoptera is missing. Utilizing single-nucleotide polymorphisms (SNPs) between two Nasonia parasitoid wasp genomes, we developed a SNP genotyping microarray to infer a high-density linkage map for Nasonia. The map comprises 1,255 markers with an average distance of 0.3 cM. The mapped markers enabled us to arrange 265 scaffolds of the Nasonia genome assembly 1.0 on the linkage map, representing 63.6% of the assembled N. vitripennis genome. We estimated a genome-wide recombination rate of 1.4-1.5 cM/Mb for Nasonia, which is less than one tenth of the rate reported for the honeybee. The local recombination rate in Nasonia is positively correlated with the distance to the center of the linkage groups, GC content, and the proportion of simple repeats. In contrast to the honeybee genome, gene density in the parasitoid wasp genome is positively associated with the recombination rate; regions of low recombination are characterized by fewer genes with larger introns and by a greater distance between genes. Finally, we found that genes in regions of the genome with a low recombination frequency tend to have a higher ratio of non-synonymous to synonymous substitutions, likely due to the accumulation of slightly deleterious non-synonymous substitutions. These findings are consistent with the hypothesis that recombination reduces interference between linked sites and thereby facilitates adaptive evolution and the purging of deleterious mutations. Our results imply that the genomes of haplodiploid and of diploid higher eukaryotes do not differ systematically in their recombination rates and associated parameters.Publisher PDFPeer reviewe

Structural insights into the autoregulation and cooperativity of the human transcription factor Ets-2

Ets-2, like its closely related homologue Ets-1, is a member of the Ets family of DNA binding transcription factors. Both proteins are subject to multiple levels of regulation of their DNA binding and transactivation properties. One such regulatory mechanism is the presence of an autoinhibitory module, which in Ets-1 allosterically inhibits the DNA binding activity. This inhibition can be relieved by interaction with protein partners or cooperative binding to closely separated Ets binding sites in a palindromic arrangement. In this study we describe the 2.5 Å resolution crystal structure of a DNA complex of the Ets-2 Ets domain. The Ets domain crystallized with two distinct species in the asymmetric unit, which closely resemble the autoinhibited and DNA bound forms of Ets-1. This discovery prompted us to re-evaluate the current model for the autoinhibitory mechanism and the structural basis for cooperative DNA binding. In contrast to Ets-1, in which the autoinhibition is caused by a combination of allosteric and steric mechanisms, we were unable to find clear evidence for the allosteric mechanism in Ets-2. We also demonstrated two possibly distinct types of cooperative binding to substrates with Ets binding motifs separated by four and six base pairs and suggest possible molecular mechanisms for this behavior

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

We acknowledge the Broad Institute Sequencing Platform and Imperial College London for generating the DNA sequence described here (and R265 Illumina sequences described previously [4]). We thank Sinéad Chapman for coordinating sequencing at the Broad Institute and Margaret Priest for assistance in submitting assemblies to NCBI. This project was supported by the National Human Genome Research Institute, grant no. U54HG003067. R.A.F. is supported by the Wellcome Trust. R.C.M. is supported by the Lister Institute for Preventive Medicine, the Medical Research Council UK, and the European Research Council.Peer reviewedPublisher PD

End-to-end model of Icelandic waters using the Atlantis framework: Exploring system dynamics and model reliability

Publisher's version (útgefin grein)Icelandic waters are very productive and the fisheries are economically important for the Icelandic nation. The importance of the fisheries has led to progressive fisheries management and extensive monitoring of the ecosystem. However, fisheries management is mainly built on single species stock assessment models, and multi-species or ecological models are essential for building capacity around ecosystem-based fisheries management. This paper describes the first end-to-end model for the Icelandic waters using the Atlantis modeling framework. The modeled area is 1,600,000 km2, and covers the area from Greenland through Icelandic waters to the Faroe Islands. The ocean area was divided into 51 spatial boxes, each with multiple vertical layers. There were 52 functional groups in the model: 20 fish groups (8 at a species level), 5 groups of mammals, 1 seabird group, 16 invertebrates, 5 primary producers, 2 bacteria and 3 detritus groups. The reliability of the model was evaluated using a skill assessment and a sensitivity analysis was conducted to understand the dynamics of the system. The sensitivity study revealed that saithe, redfish and tooth whales had the greatest effect on other groups in the system. The skill assessment showed that the model was able to replicate time-series of biomass and landings for the most important commercial groups and that modeling of the recruitment processes was important for some of the groups. This model now provides a solid basis for evaluating alternative ecosystem and fisheries management scenarios, and should produce reliable results for the most important commercial groups.This study has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 613571 for the project MareFrame and from the European Commission’s Horizon 2020 Research and Innovation Programme under Grant Agreement No. 634495 for the project Science, Technology, and Society Initiative to minimize Unwanted Catches in European Fisheries (Minouw). Funding from the Icelandic Research Fund (rannis, No. 152039051) is also acknowledged.Peer Reviewe

Genome Diversity, Recombination, and Virulence across the Major Lineages of Paracoccidioides

We thank Angela Restrepo, Rosana Puccia, Zoilo Pires de Camargo, and Maria Sueli Felipe for kindly providing the isolates for this study. This project has been funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under contract no. HHSN272200900018C. This work was partly supported by Colciencias via the grants “A Gene Atlas for Human Pathogenic Fungi” (122256934875) and “A Comprehensive Genomic and Transcriptomic Analysis of Dimorphic Human Pathogen Fungi and Its Relation with Virulence” (221365842971) and by the Universidad de Antioquia via a “Sostenibilidad 2015/2016” grant. Colciencias National Doctorate Program funding supported J.F.M.; Enlaza Mundos partly supported his fellowship. The Wellcome Trust supported R.A.F.Peer reviewedPublisher PD