Re-Evaluating Botryosphaeriales: Ancestral State Reconstructions of Selected Characters and Evolution of Nutritional Modes.

Botryosphaeriales (Dothideomycetes, Ascomycota) occur in a wide range of habitats as endophytes, saprobes, and pathogens. The order Botryosphaeriales has not been subjected to evaluation since 2019 by Phillips and co-authors using phylogenetic and evolutionary analyses. Subsequently, many studies introduced novel taxa into the order and revised several families separately. In addition, no ancestral character studies have been conducted for this order. Therefore, in this study, we re-evaluated the character evolution and taxonomic placements of Botryosphaeriales species based on ancestral character evolution, divergence time estimation, and phylogenetic relationships, including all the novel taxa that have been introduced so far. Maximum likelihood, maximum parsimony, and Bayesian inference analyses were conducted on a combined LSU and ITS sequence alignment. Ancestral state reconstruction was carried out for conidial colour, septation, and nutritional mode. Divergence times estimates revealed that Botryosphaeriales originated around 109 Mya in the early epoch of the Cretaceous period. All six families in Botryosphaeriales evolved in the late epoch of the Cretaceous period (66-100 Mya), during which Angiosperms also appeared, rapidly diversified and became dominant on land. Families of Botryosphaeriales diversified during the Paleogene and Neogene periods in the Cenozoic era. The order comprises the families Aplosporellaceae, Botryosphaeriaceae, Melanopsaceae, Phyllostictaceae, Planistromellaceae and Saccharataceae. Furthermore, current study assessed two hypotheses; the first one being "All Botryosphaeriales species originated as endophytes and then switched into saprobes when their hosts died or into pathogens when their hosts were under stress"; the second hypothesis states that "There is a link between the conidial colour and nutritional mode in botryosphaerialean taxa". Ancestral state reconstruction and nutritional mode analyses revealed a pathogenic/saprobic nutritional mode as the ancestral character. However, we could not provide strong evidence for the first hypothesis mainly due to the significantly low number of studies reporting the endophytic botryosphaerialean taxa. Results also showed that hyaline and aseptate conidia were ancestral characters in Botryosphaeriales and supported the relationship between conidial pigmentation and the pathogenicity of Botryosphaeriales species.

The split genes of Nanoarchaeum equitans have not originated in its lineage and have been merged in another Nanoarchaeota: a reply to Podar et al.

I reply to the suggestion of Podar et al. (2013) that the split genes of Nanoarchaeun equitans are a derived character, showing that their analysis is mistaken. In particular, I show that the split genes both proteins and tRNAs have not been split in N. equitans and have been on the contrary merged in the nanoarchaeon sequenced recently by Podar et al. (2013). This implies that the main argument of Podar et al. (2013) that there should be: "a unique propensity for splitting in the Nanoarchaeota that is most dramatically manifested in the Nanoarchaeum equitans lineage" is false. On the other hand, the analysis seems to favor the hypothesis that the split genes are an ancestral character. This would strengthen to greater extent a model for the origin of the tRNA molecule.