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LOSS OF FUNCTION GENES. “Firstly, these mutations tend to be on terminal branches of the gene tree. Secondly, pseudogenes rarely accumulate many loss-of-function mutations. Although this suggests that cifA and cifB pseudogenes rarely codiverge with the Wolbachia genome for long periods, it is unclear whether this results from the loss of the Wolbachia infection or through the genes being deleted from the genome, for instance, by phage excision.” https://lnkd.in/dXjWp9f View in LinkedIn

HOMOLOGY. “Given the relative homogeneity of cifA domains and the similarities of these additional cifB domains with known toxins and eukaryotic-like ankyrin proteins, it is tempting to hypothesize that they are linked to the modification function by interacting with the host rather than the binding to cifA.” https://lnkd.in/dXjWp9f View in LinkedIn

FOLLOWING THE BREADCRUMBS. “In the absence of other phenotypic effects on the host, theory predicts that the loss-of-sperm modification will lead to the loss of Wolbachia from the host population. We found that the majority of loss-of-function mutations appears to have occurred recently.” https://lnkd.in/dXjWp9f View in LinkedIn

UNRESOLVED ANSWER. “However, we found no evidence for this, and frequently paralogs within the same genome are closely related. We would argue that this does not mean that we should discount the hypothesis that cif paralogs accumulate within the same genome because they encode bidirectionally incompatible CI factors.” (CI = cytoplasmic incompatibility). https://lnkd.in/dXjWp9f View in LinkedIn

DIRECTIONALITY HYPOTHESIS. “This is because females harboring additional Wolbachia strains will be compatible with all males in the population. An equivalent process will promote the invasion and maintenance of cif paralogs within the same genome, provided that they encode bidirectionally incompatible modification and rescue factors. If bidirectionally incompatibility evolves gradually, this hypothesis predicts that paralogous cif genes within a genome might be distantly related.” https://lnkd.in/dXjWp9f View in LinkedIn

GENERIC DIVERSITY. “Wolbachia genomes often carry multiple cifA–cifB gene pairs. This is analogous to the frequent occurrence of multiple Wolbachia strains within the same host individuals. Both experimental and theoretical studies have demonstrated that such multiple infections can invade host populations provided the strains carry different modification and rescue factors.” https://lnkd.in/dXjWp9f View in LinkedIn

LAYERED PIGGYBACK. “Indeed, cif genes that lose their association with mobile elements may ultimately go extinct as they would be less likely to undergo horizontal transfer. As argued by Beckmann, Bonneau, et al. (2019), in some cases CI may be best viewed as an adaptation of mobile genetic elements to spread within Wolbachia populations.” (CI = cytoplasmic incompatibility). https://lnkd.in/dXjWp9f View in LinkedIn

MINOR PLAYER. “However, this does not mean that phages are not a major route of horizontal transmission of cif genes, and the association between cif genes and mobile genetic elements supports the idea that the ability to move horizontally between genomes may be an important adaptation of these elements.” https://lnkd.in/dXjWp9f View in LinkedIn

UNCORRELATED. “Interestingly, Lepage et al. (2017) found no significant association between the phylogenies of cif genes and genes found in the structural module of phages. Prophage regions often rearrange which likely explains this pattern.” https://lnkd.in/dXjWp9f View in LinkedIn

ASSISTANCE FROM OTHER PLAYERS. “Horizontal transfer of cif genes occurs frequently and sometimes over large phylogenetic distances, sometimes even crossing the bacterial genus boundaries. High rates of horizontal transfer likely result from the cif genes being associated with mobile genetic elements, such as WO prophage sequences, transposons, and plasmids.” https://lnkd.in/dXjWp9f View in LinkedIn