Biology subjects

Francis M Jiggins

Publications and source records attributed to Francis M Jiggins.

3 recordsLinked to original sources

bioRxiv2016

Natural selection and genetic diversity in the butterfly Heliconius melpomene

A combination of selective and neutral evolutionary forces shape patterns of genetic diversity in nature. Among the insects, most previous analyses of the roles of drift and selection in shaping variation across the genome have focused on the genus Drosophila. A more complete understanding of these forces will come from analysing other taxa that differ in population demography and other aspects of biology. We have analysed diversity and signatures of selection in the neotropical Heliconius butterflies using resequenced genomes from 58 wild-caught individuals of H. melpomene, and another 21 resequenced genomes representing 11 related species. By comparing intra-specific diversity and inter-specific divergence, we estimate that 31% of amino acid substitutions between Heliconius species are adaptive. Diversity at putatively neutral sites is negatively correlated with the local density of coding sites as well as non-synonymous substitutions, and positively correlated with recombination rate, indicating widespread linked selection. This process also manifests in significantly reduced diversity on longer chromosomes, consistent with lower recombination rates. Although hitchhiking around beneficial non-synonymous mutations has significantly shaped genetic variation in H. melpomene, evidence for strong selective sweeps is limited overall. We did however identify two regions where distinct haplotypes have swept in different populations, leading to increased population differentiation. On the whole, our study suggests that positive selection is less pervasive in these butterflies as compared to fruit flies; a fact that curiously results in very similar levels of neutral diversity in these very different insects.

Evolutionary Biology↗

bioRxiv2015

The evolution, diversity and host associations of rhabdoviruses

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.

Evolutionary Biology↗

bioRxiv2014

Comparative genomics reveals the origins and diversity of arthropod immune systems

While the innate immune system of insects is well-studied, comparatively little is known about how other arthropods defend themselves against infection. We have characterised key immune components in the genomes of five chelicerates, a myriapod and a crustacean. We found clear traces of an ancient origin of innate immunity, with some arthropods havingToll-like receptors and C3-complement factors that are more closely related in sequence or structure to vertebrates than other arthropods. Across the arthropods some components of the immune system, like the Toll signalling pathway, are highly conserved. However, there is also remarkable diversity. The chelicerates apparently lack the Imd signalling pathway and BGRPs - a key class of pathogen recognition receptors. Many genes have large copy number variation across species, and this may sometimes be accompanied by changes in function. For example, peptidoglycan recognition proteins (PGRPs) have frequently lost their catalytic activity and switch between secreted and intracellular forms. There has been extensive duplication of the cellular immune receptor Dscam in several species, which may be an alternative way to generate the high diversity that produced by alternativesplicing in insects. Our results provide a detailed analysis of the immune systems of several important groups of animals and lay the foundations for functional work on these groups.

Evolutionary Biology↗