Adaptive evolution of interferon induced protein with tetratricopeptide repeats 5(IFIT5) in birds

Background : Previous studies have revealed that wild birds are reservoirs and mobile vectors of viruses, many of which cause illness and mortality in domestic bird and humans. In birds, the invasion of viruses will quickly trigger the innate immune mechanism induced by interferon (IFN). As IFN-stimulated genes (ISGs), the IFIT gene family plays an important role in innate immunity. However, only IFIT5 of the IFIT gene family exists in birds, and the direction and strength of selection acting on IFIT5 are largely unknown. Results : Here, we studied the selection on IFIT5 based on the coding sequence (CDS) data of 20 birds. We identified 12 persistent positive selection sites (PSS), other sites suffered purifying selection and neutral selection; probably due to functional constraints. We also found humans have only 3PSS (189,197and 295), likely due to having more IFIT gene family member that can cooperate to resist virus invasion. The 12 PSS located in the closed clamp structure of the IFIT5 protein, except for position 45. In particular, 3 PSS (335, 342 and 367) were located in the TPR domain, which implied their important roles in virus recognition. We only found 2 episodic PSS (30,332) in Passeriformes, indicating episodic selection pressure in Passeriformes lineage. The positive selection of IFIT5 might provide a theoretical basis for the pathogen-host interaction in birds. Conclusions : We found that the diversity of IFIT5 domains in birds, and that the PSS of IFIT5 is the joint influence of functional domain conservation and the pressure of virus evolution.We speculated that persistent PSS may affect the antiviral function of IFIT5, especially in the region of closed clamp structure. These results lay a theoretical foundation for the further study of the antiviral immune mechanism of IFIT5 in birds.

Strong Episodic Selection for Natural Competence for Transformation Due to Host-Pathogen Dynamics

Sexual recombination only occurs in eukaryotes; however, many bacteria can actively recombine with environmental DNA. This behavior, referred to as transformation, has been described in many species from diverse taxonomic backgrounds. Transformation is hypothesized to carry some selective advantages similar to those postulated for meiotic sex in eukaryotes. However, the accumulation of loss-of-function alleles at transformation loci and an increased mutational load from recombining with DNA from dead cells create additional costs to transformation. These costs have been shown to outweigh many of the benefits of recombination under a variety of likely parameters. We investigate an additional proposed benefit of sexual recombination, the Red Queen hypothesis, as it relates to bacterial transformation. Here we describe a model showing that host-pathogen coevolution may provide a large selective benefit to transformation and allow transforming cells to invade an environment dominated by otherwise equal non-transformers. Furthermore, we observe that host-pathogen dynamics cause the selection pressure on transformation to vary extensively in time, potentially explaining the tight regulation and wide variety of rates observed in naturally competent bacteria. Host-pathogen dynamics may explain the evolution and maintenance of natural competence despite its associated costs.

Revisiting the evolutionary analysis of mammalian CRISPs reveals positive selection

Cysteine-rich secretory proteins (CRISPs) constitute a versatile family, with functions that include being components of reptilian venom and participation in mammalian reproduction. While non-mammalian vertebrates express a single CRISP gene, mammals generally express three CRISP paralogs. A previous study assessing the molecular evolution of vertebrate CRISPs revealed strong positive selection in reptilian CRISP and negative selection in mammalian CRISPs. In this study, we re-assessed molecular adaptation of mammalian CRISPs through an analysis of larger sequence datasets that represent mammalian diversity. Our analyses show evidence of recent episodes of positive selection for all mammalian CRISPs. Intensity of positive selection was heterogeneous both among CRISP paralogs (being stronger in CRISP3 than in CRISP1 and CRISP2) and across functional domains (having more impact on CRD or PR-1 domain). Analysis of episodic selection did not yield strong signatures of adaptive evolution in any particular mammalian group, suggesting that positive selection was more pervasive on mammalian CRISPs. Our findings provide evidence of adaptive evolution in a family of reproduction-related proteins, and offer interesting insights regarding the role of mammalian CRISPs in fertility and speciation.

Rapid genome sequencing for outbreak analysis of the emerging human fungal pathogen Candida auris

BackgroundCandida auris was first described in 2009, and has since caused nosocomial outbreaks, invasive infections and fungaemia across 11 countries in five continents. An outbreak of C. auris occurred in a specialised cardiothoracic London hospital between April 2015 and November 2016, which to date has been the largest outbreak reported worldwide, involving a total of 72 patients.MethodsTo understand the epidemiology of C. auris infection within this hospital, we sequenced the genomes of outbreak isolates using Oxford Nanopore Technologies and Illumina in order to type antifungal resistance alleles and to explore the outbreak within its local and global context.FindingsPhylogenomic analysis placed the UK outbreak in the India/Pakistan clade, demonstrating an Asian origin. The outbreak showed similar diversity to that of the entire clade and limited local spatiotemporal clustering was observed. One isolate displayed resistance to both echinocandins and 5-flucytosine; the former was associated with a serine to tyrosine amino acid substitution in the gene FKS1, and the latter was associated with a phenylalanine to isoleucine substitution in the gene FUR1. These mutations are novel for this pathogen.InterpretationMultiple differential episodic selection of antifungal resistant genotypes has occurred within a genetically heterogenous population across this outbreak, creating a resilient pathogen and making it difficult to define local-scale patterns of transmission as well as implementing outbreak control measures.FundingAntimicrobial Research Collaborative, Imperial College London

Population Structure of Dogwood Anthracnose Fungus

Dogwood anthracnose, caused by Discula destructiva, affects several native dogwood species in North America, especially flowering dogwood in the east and Pacific dogwood in the west. The fungus behaves as a recently introduced plant pathogen under episodic selection. Two distinct disjunct groups of fungal isolates corresponding to eastern and western groups were detected by amplified fragment length polymorphisms and sequences of the intergenic spacer (IGS) of the nuclear ribosomal DNA, translation elongation factor-1α, and β-tubulin genes. Of 20 genotypes identified among 72 isolates, 17 genotypes were from the eastern United States (n = 50), but only three were present among the western isolates (n = 22), indicating that the eastern population may be more diverse. Most eastern and western isolates belonged to a few widespread clones, and the genetic variability of this apparently asexual fungus was remarkably low compared with that of many other asexual fungi. We conclude that D. destructiva is still under intense selection pressure and that episodic selection may still be in effect. The New York City area, a possible epidemic center in the east, had relatively higher genetic variability than samples from other areas.

Episodic selection as a force in fungal microevolution, with special reference to clonal speciation and hybrid introgression

Episodic selection encompasses any sudden environmental disturbance likely to lead to a significant alteration in a species' population structure. Such disturbances include geographical transposition, a change in substrate availability, exposure to a new host or a new vector, climate change, and pollution stress. Today, such events may often be brought about by man. Their role in the promotion of fungal microevolution is discussed. In some circumstances, episodic selection may result in the emergence of a highly fitted clone from an originally heterogeneous population, and sustained disturbance may lead to clonal speciation. Clonal speciation accompanied by loss of sexual function, whether under episodic selection or under less intensive but analagous environmental conditions, could account for the origin of many of today's imperfect taxa (Deuteromycotina). Geographical transposition, a special form of episodic selection, can lead to hybridization between previously allopatric species. This may result in modifications to existing species via the acquisition of new loci or cytoplasmic elements, in the production of new taxa via secondary speciation, or in the emergence of hybrid swarms. Episodic selection will also favour survival of novel genotypes by providing new habitats for exploitation, so encouraging novel evolutionary development. Key words: episodic selection, fungal speciation, hybridization, introgression.