A document by Jianhai Chen. Click on the document to view its contents.

Gyrodactylus is a lineage of monogenean flatworm ectoparasites exhibiting many features that make them a suitable model to study their co-evolution with fish hosts. Previous co-evolutionary studies of this lineage mainly relied on low-power datasets (a small number of samples and a single molecular marker), and (now) outdated algorithms. To investigate the coevolutionary relationship of gyrodactylids and their fish hosts in high resolution, we used complete mitogenomes (including two newly sequenced Gyrodactylus species), a large number of species in the single-gene dataset, and four different coevolutionary algorithms. The overall co-evolutionary fit between the parasites and hosts was consistently significant. Multiple indicators support gyrodactylids as highly host-specific parasites, but few gyrodactylids can parasitize either multiple (more than 5) or phylogenetically-distant fish hosts. The molecular dating results indicate they tend to evolve towards high host specificity. Speciation by host-switching is a more important speciation mode than co-speciation for them. Assuming the origin on Cypriniformes, we inferred four major host switch events to non-Cypriniformes hosts (mostly Salmoniformes) occurred deep in the evolutionary history. Despite their relative rarity, these events had strong macroevolutionary consequences for gyrodactylid diversity. For example, in our dataset, 57.28% of all studied gyrodactylids parasitised only non-Cypriniformes hosts, which implies that the evolutionary history of more than half of all included lineages could be traced back to these major host switch events. Geographical co-occurrence of fishes and gyrodactylids determined the host use by these gyrodactylids, and geography accounted for most of the phylogenetic signal in host use.

Rhesus macaque (Macaca mulatta) is the most extensively studied nonhuman primate species for human biomedical modeling. However, little is known about the biological pattern of genome-wide structural variations (SVs) and the evolutionary forces underlying SVs in this species. Here, we conducted genomic sequencing and analyses based on Nanopore long-reads and Illumina short-reads technologies. We called SVs between the two subspecies (China vs. India), using three methods of assembly-based and long-reads-based algorithms. Interestingly, we found significantly more SVs in the X-chromosome than in autosomes, consistent with the expectation of the faster-X divergence at the subspecies level. With the fine-scale methylation frequencies and recombination rates, we found duplications with significantly lower methylation frequencies while higher recombination rates than other types of SVs, suggesting a higher level of transcriptional and evolutionary potential for duplications than for other SVs types. A genome-wide scan of selective sweeps revealed that over 3% of SVs are under positive selection and that X chromosome showed significantly higher number of positively selected SVs than do autosomes, suggesting the “faster-X effect” of SVs. Thus, our study revealed a different evolutionary importance of duplications compared with other SVs forms in producing raw material upon which selective forces, including the faster-X effect, can further play.

The arms race between humans and pathogens drives the evolution of the human genome. Here, based on the HPO (Human Phenotype Ontology) annotation, we focused on human genes related to recurrent infections of virus, (RVI), bacterial (RBI) and recurrent fungal infections (RFI) to understand positive selection on pathogen-responsive genes. Interestingly, cross-species positive selection analyses revealed that the proportion of unique genes under positive selection was higher for RVI (78.57%) than for RFI (57.14%) and RBI (58.68%). Based on results of the branch-site test, we further focused on the amino acid site Val129 of IRF9, which has a significant signal of positive selection based on multiple evidence. Interestingly, this novel and derived amino acid (V) has been rapidly fixed before the “out-of-Africa” event ~500,000 years ago from the ancestral state S, which is conserved among 88.5% of mammalian lineages. Phosphorylation analysis revealed that the conserved ancestral S may serve as the phosphorylation site of IRF9. Further analyses suggested that the rapid dephosphorylation of IRF9 via the change of S to V may have conferred potential molecular adaptations by boosting and extending the immune activity of IRF9. This study provides an interesting mode in which strong positive Darwinian selection drives the rapid fixation of a hominin specific amino acid leading to molecular adaptation for immune response.