Incomplete lineage sorting and hybridization underlie tree discordance in Petunia and related genera (Petunieae, Solanaceae).

Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.

Transcription Factors Evolve Faster Than Their Structural Gene Targets in the Flavonoid Pigment Pathway.

Dissecting the relationship between gene function and substitution rates is key to understanding genome-wide patterns of molecular evolution. Biochemical pathways provide powerful systems for investigating this relationship because the functional role of each gene is often well characterized. Here, we investigate the evolution of the flavonoid pigment pathway in the colorful Petunieae clade of the tomato family (Solanaceae). This pathway is broadly conserved in plants, both in terms of its structural elements and its MYB, basic helix-loop-helix, and WD40 transcriptional regulators, and its function has been extensively studied, particularly in model species of petunia. We built a phylotranscriptomic data set for 69 species of Petunieae to infer patterns of molecular evolution across pathway genes and across lineages. We found that transcription factors exhibit faster rates of molecular evolution (dN/dS) than their targets, with the highly specialized MYB genes evolving fastest. Using the largest comparative data set to date, we recovered little support for the hypothesis that upstream enzymes evolve slower than those occupying more downstream positions, although expression levels do predict molecular evolutionary rates. Although shifts in floral pigmentation were only weakly related to changes affecting coding regions, we found a strong relationship with the presence/absence patterns of MYB transcripts. Intensely pigmented species express all three main MYB anthocyanin activators in petals, whereas pale or white species express few or none. Our findings reinforce the notion that pathway regulators have a dynamic history, involving higher rates of molecular evolution than structural components, along with frequent changes in expression during color transitions.

Supergroup F Wolbachia in terrestrial isopods: Horizontal transmission from termites?

Horizontal transmission between distantly related species has been used to explain how Wolbachia infect multiple species at astonishing rates despite the selection for resistance. Recently, a terrestrial isopod species was found to be infected by an unusual strain of supergroup F Wolbachia. However, only Wolbachia of supergroup B is typically found in isopods. One possibility is that these isopods acquired the infection because of their recurrent contact with termites-a group with strong evidence of infection by supergroup F Wolbachia. Thus, our goals were: (1) check if the infection was an isolated case in isopods, or if it revealed a broader pattern; (2) search for Wolbachia infection in the termites within Brazil; and (3) look for evidence consistent with horizontal transmission between isopods and termites. We collected Neotroponiscus terrestrial isopods and termites along the Brazilian coastal Atlantic forest. We sequenced and identified the Wolbachia strains found in these groups using coxA, dnaA, and fpbA genes. We constructed phylogenies for both bacteria and host taxa and tested for coevolution. We found the supergroup F Wolbachia in other species and populations of Neotroponiscus, and also in Nasutitermes and Procornitermes termites. The phylogenies showed that, despite the phylogenetic distance between isopods and termites, the Wolbachia strains clustered together. Furthermore, cophylogenetic analyses showed significant jumps of Wolbachia between terrestrial isopods and termites. Thus, our study suggests that the horizontal transmission of supergroup F Wolbachia between termites and terrestrial isopods is likely. Our study also helps understanding the success and worldwide distribution of this symbiont. SUPPLEMENTARY INFORMATION: The online version of this article (10.1007/s10682-021-10101-4) contains supplementary material, which is available to authorized users.