Metagenomic studies are leading to the discovery of a hidden diversity of RNA viruses. These new viruses are poorly characterised and new approaches are needed predict the host species these viruses pose a risk to. The rhabdoviruses are a diverse family of RNA viruses that includes important pathogens of humans, animals and plants. We have discovered 32 new rhabdoviruses through a combination of our own RNA sequencing of insects and searching public sequence databases. Combining these with previously known sequences we reconstructed the phylogeny of 195 rhabdovirus sequences, and produced the most in depth analysis of the family to date. In most cases we know nothing about the biology of the viruses beyond the host they were identified from, but our dataset provides a powerful phylogenetic approach to predict which are vector-borne viruses and which are specific to vertebrates or arthropods. By reconstructing ancestral and present host states we found that switches between major groups of hosts have occurred rarely during rhabdovirus evolution. This allowed us to propose 76 new likely vector-borne vertebrate viruses among viruses identified from vertebrates or biting insects. Based on currently available data, our analysis suggests it is likely there was a single origin of the known plant viruses and arthropod-borne vertebrate viruses, while vertebrate-specific and arthropod-specific viruses arose at least twice. There are also few transitions between aquatic and terrestrial ecosystems. Viruses also cluster together at a finer scale, with closely related viruses tending to be found in closely related hosts. Our data therefore suggest that throughout their evolution, rhabdoviruses have occasionally jumped between distantly related host species before spreading through related hosts in the same environment. This approach offers a way to predict the most probable biology and key traits of newly discovered viruses.
Evolution of complex phenotypes through successions of adaptive steps
Tin Y. Pang, Martin Lercher
The emergence of complex phenotype is a fascinating question of evolutionary biology, and we sought to understand preadaptation which facilitated the development of complex phenotypes, in the context of bacterial metabolic network. Genes coordinated for a phenotype are likely to cluster on the same place of the genome, which so allows horizontal gene transfer (HGT) to pass the phenotype to another bacterium. But for a complex phenotype, its genes are clustered on different places of the genome cannot be transferred adaptively; it is preadaptation, which refers to adaptive transfer of a segment relevant to a complex phenotype for other purposes, that allows it later to be recruited for the complex phenotype. To search for preadaptation in the evolutionary history of E. coli, we reconstructed the ancestral genomes from various strains, identified the transferred genes, grouped them into possible transferred segments, and analyzed the gains in nutritional phenotypes corresponding to the acquisitions of segments of metabolic genes. Properties of these HGT segments inferred from data are enumerated and compared with a model of HGT, which shows that: 1) HGT segments are likely to adaptive, and segments carrying reactions essential to phenotypic gains but non-adaptive are rare; 2) the landscape of segment transfer for complex phenotypes is directional and path-dependent; 3) cooperation between HGT segments to support various nutritional phenotypes are observed to be more frequent than expected, which serves as an evidence to preadaptation in the evolution of bacterial metabolic network.
Wolbachia infection in a sex-structured mosquito population carrying West Nile virus
József Z. Farkas, Stephen A. Gourley, Rongsong Liu, Abdul-Aziz Yakubu
Wolbachia is possibly the most studied reproductive parasite of arthropod species. It appears to be a promising candidate for biocontrol of some mosquito borne diseases. We begin by developing a sex-structured model for a Wolbachia infected mosquito population. Our model incorporates the key effects of Wolbachia infection including cytoplasmic incompatibility and male killing. We also allow the possibility of reduced reproductive output, incomplete maternal transmission, and different mortality rates for uninfected/infected male/female individuals. We study the existence and local stability of equilibria, including the biologically relevant and interesting boundary equilibria. For some biologically relevant parameter regimes there may be multiple coexistence steady states including, very importantly, a coexistence steady state in which Wolbachia infected individuals dominate. We also extend the model to incorporate West Nile virus (WNv) dynamics, using an SEI modelling approach. Recent evidence suggests that a particular strain of Wolbachia infection significantly reduces WNv replication in Aedes aegypti. We model this via increased time spent in the WNv-exposed compartment for Wolbachia infected female mosquitoes. A basic reproduction number R0 is computed for the WNv infection. Our results suggest that, if the mosquito population consists mainly of Wolbachia infected individuals, WNv eradication is likely if WNv replication in Wolbachia infected individuals is sufficiently reduced.