Intronic hammerhead ribozymes are ultraconserved in the human genome

Small ribozymes have been regarded as living fossils of a prebiotic RNA world that would have remained in the genomes of modern organisms. In this study, we report the ultraconserved occurrence of hammerhead ribozymes in Amniota genomes (reptiles, birds and mammals, including humans), similar to those described previously in amphibians and platyhelminth parasites. The ribozymes mapped to intronic regions of different genes, such as the tumour suppressor RECK in birds and mammals, a mammalian tumour antigen and the dystrobrevin beta in lizards and birds. In vitro characterization confirmed a high self-cleavage activity, whereas analysis of RECK-expressed sequence tags revealed fusion events between the in vivo self-cleaved intron and U5 or U6 small nuclear RNA fragments. Together, these results suggest a conserved role for these ribozymes in messenger RNA biogenesis.     

Pre-adaptation and adaptation shape trait-environment matching in the Neotropics

Aim

Functional traits shape the distribution of taxa across environments. However, it remains unclear whether trait and environmental niche evolution are correlated, and what happened first: trait change facilitating environment shifts (pre-adaptation) or environmental change leading to trait change (adaptation). We focus on a species-rich Neotropical legume radiation to shed light on this enigma.

Location

Neotropics.

Time Period

Cenozoic.

Major Taxa Studied

Fabaceae: Papilionoidae: Swartzia.

Methods

We assembled leaflet, fruit and petal size data from monographs and herbarium collections for 86 to 96% of the c. 180 Swartzia species, inferred a dated Swartzia phylogenetic tree from existing DNA sequences covering 38% of the species and integrated these with distribution, soil and climate data. We used phylogenetic linear regression to quantify trait–environment relationships and applied comparative methods to evaluate modes of correlated evolution between traits and environments.

Results

Leaflet and petal size were strongly linked to climate, while fruit size was not associated with climate or soil characteristics. Evolutionary transitions to relatively low rainfall and low temperature environments were conditional on the evolution of small leaflets, whereas transitions to wet and warm environments were preceded by the evolution of larger leaflets. In contrast, transitions to the warmest or coldest environments were followed, rather than preceded, by petal loss.

Main Conclusion

Our results show that the macroevolution of functional traits has influenced the broad-scale distribution of Swartzia across Neotropical rainforest, seasonally dry, montane and inundated habitats. We suggest that trait evolution is conditional on environmental change but both pre-adaptive and adaptive processes may occur. These processes are important to understand the distribution of diversity at both regional (e.g. Amazonia) and global biogeographical scales.     

Discovery of a novel long terminal repeat (LTR2i_SS) in Sus Scrofa

Long terminal repeat (LTR) retrotransposons are transposable elements flanked by 5′/3′ LTRs. They have a structure similar to endogenous retroviruses, but they lack the envelope (env) gene making them non‐infectious. Long terminal repeats are motif‐rich sequences and can act as bidirectional promoters or enhancers to regulate or inactivate genes by insertion. In this study, we identified a new chimeric LTR subfamily, LTR2i_SS, in the pig genome. This chimeric LTR family appears to be the ancestral form of the previously described LTR2_SS family. LTR2_SS appears to have deleted ~300 bp of un‐annotated, ancestral sequence from LTR2i_SS. We identified no functional provirus sequences for either of these LTR types. LTR2i_SS sequences have been exapted into the untranslated regions of two protein‐coding gene mRNAs. Both of these genes lie within previously mapped pig quantitative trait loci.     

As a toxin dies a prion comes to life: A tentative natural history of the [Het-s] prion

A variety of signaling pathways, in particular with roles in cell fate and host defense, operate by a prion-like mechanism consisting in the formation of open-ended oligomeric signaling complexes termed signalosomes. This mechanism emerges as a novel paradigm in signal transduction. Among the proteins forming such signaling complexes are the Nod-like receptors (NLR), involved in innate immunity. It now appears that the [Het-s] fungal prion derives from such a cell-fate defining signaling system controlled by a fungal NLR. What was once considered as an isolated oddity turns out to be related to a conserved and widespread signaling mechanism. Herein, we recall the relation of the [Het-s] prion to the signal transduction pathway controlled by the NWD2 Nod-like receptor, leading to activation of the HET-S pore-forming cell death execution protein. We explicit an evolutionary scenario in which formation of the [Het-s] prion is the result of an exaptation process or how a loss-of-function mutation in a pore-forming cell death execution protein (HET-S) has given birth to a functional prion ([Het-s]).     

Comprehensive analysis of endogenous bornavirus-like elements in eukaryote genomes

Bornaviruses are the only animal RNA viruses that establish a persistent infection in their host cell nucleus. Studies of bornaviruses have provided unique information about viral replication strategies and virus–host interactions. Although bornaviruses do not integrate into the host genome during their replication cycle, we and others have recently reported that there are DNA sequences derived from the mRNAs of ancient bornaviruses in the genomes of vertebrates, including humans, and these have been designated endogenous borna-like (EBL) elements. Therefore, bornaviruses have been interacting with their hosts as driving forces in the evolution of host genomes in a previously unexpected way. Studies of EBL elements have provided new models for virology, evolutionary biology and general cell biology. In this review, we summarize the data on EBL elements including what we have newly identified in eukaryotes genomes, and discuss the biological significance of EBL elements, with a focus on EBL nucleoprotein elements in mammalian genomes. Surprisingly, EBL elements were detected in the genomes of invertebrates, suggesting that the host range of bornaviruses may be much wider than previously thought. We also review our new data on non-retroviral integration of Borna disease virus.     

A phylogenetic test for adaptive convergence in rock-dwelling lizards

Phenotypic similarity of species occupying similar habitats has long been taken as strong evidence of adaptation, but this approach implicitly assumes that similarity is evolutionarily derived. However, even derived similarities may not represent convergent adaptation if the similarities did not evolve as a result of the same selection pressures; an alternative possibility is that the similar features evolved for different reasons, but subsequently allowed the species to occupy the same habitat, in which case the convergent evolution of the same feature by species occupying similar habitats would be the result of exaptation. Many lizard lineages have evolved to occupy vertical rock surfaces, a habitat that places strong functional and ecological demands on lizards. We examined four clades in which species that use vertical rock surfaces exhibit long hindlimbs and flattened bodies. Morphological change on the phylogenetic branches leading to the rock-dwelling species in the four clades differed from change on other branches of the phylogeny; evolutionary transitions to rock-dwelling generally were associated with increases in limb length and decreases in head depth. Examination of particular characters revealed several different patterns of evolutionary change. Rock-dwelling lizards exhibited similarities in head depth as a result of both adaptation and exaptation. Moreover, even though rock-dwelling species generally had longer limbs than their close relatives, clade-level differences in limb length led to an overall lack of difference between rock- and non-rock-dwelling lizards. These results indicate that evolutionary change in the same direction in independent lineages does not necessarily produce convergence, and that the existence of similar advantageous structures among species independently occupying the same environment may not indicate adaptation.     

Endozoochory and Fire as Germination Triggers in Neotropical Dry Forests: an Experimental Test

Endozoochory and fire are crucial ecological factors determining germination success and recruitment in many plant species. Fire is a well‐known germination trigger while endozoochory may allow seed dispersal along with an increase in germination. Their interaction has rarely been addressed, however, even though both factors are pervasive in human‐transformed ecosystems like most Neotropical Dry Forests (NDF). For three common Mesoamerican tree species (Acacia pennatula, Enterolobium cyclocarpum, and Guazuma ulmifolia), we used feeding trials to assess the preference of cattle, which are their main seed dispersal agent. We also experimentally tested the interaction between gut passage and fire as triggers of germination. The fruits of the three species were eaten by cattle, but the small seeds of G. ulmifolia were ingested 10‐fold more than those of the other species. While gut passage did not have any effect on germination, heat‐shocks above 90 °C increased the number of germinating seeds by 15 percent. These results suggest that cattle may be a key dispersal vector in NDF, but that fire may be an important germination trigger. Physical dormancy in these species may have been selected for by extinct megaherbivores because it was a key trait ensuring seed survival after gut passage. However, in light of the recent expansion of cattle‐ranching and fire occurrence in NDF, it has become a useful exaptation facilitating the colonization of disturbed areas.