Continued adaptation of C4 photosynthesis after an initial burst of changes in the andropogoneae grasses

C4 photosynthesis is a complex trait that sustains fast growth and high productivity in tropical and subtropical conditions and evolved repeatedly in flowering plants. One of the major C4 lineages is Andropogoneae, a group of ∼ 1,200 grass species that includes some of the world's most important crops and species dominating tropical and some temperate grasslands. Previous efforts to understand C4 evolution in the group have compared a few model C4 plants to distantly related C3 species, so that changes directly responsible for the transition to C4 could not be distinguished from those that preceded or followed it. In this study, we analyse the genomes of 66 grass species, capturing the earliest diversification within Andropogoneae as well as their C3 relatives. Phylogenomics combined with molecular dating and analyses of protein evolution show that many changes linked to the evolution of C4 photosynthesis in Andropogoneae happened in the Early Miocene, between 21 and 18 Ma, after the split from its C3 sister lineage, and before the diversification of the group. This initial burst of changes was followed by an extended period of modifications to leaf anatomy and biochemistry during the diversification of Andropogoneae, so that a single C4 origin gave birth to a diversity of C4 phenotypes during 18 million years of speciation events and migration across geographic and ecological spaces. Our comprehensive approach and broad sampling of the diversity in the group reveals that one key transition can lead to a plethora of phenotypes following sustained adaptation of the ancestral state

Phylogenomics and the rise of the angiosperms

Angiosperms are the cornerstone of most terrestrial ecosystems and human livelihoods1,2. A robust understanding of angiosperm evolution is required to explain their rise to ecological dominance. So far, the angiosperm tree of life has been determined primarily by means of analyses of the plastid genome3,4. Many studies have drawn on this foundational work, such as classification and first insights into angiosperm diversification since their Mesozoic origins5,6,7. However, the limited and biased sampling of both taxa and genomes undermines confidence in the tree and its implications. Here, we build the tree of life for almost 8,000 (about 60%) angiosperm genera using a standardized set of 353 nuclear genes8. This 15-fold increase in genus-level sampling relative to comparable nuclear studies9 provides a critical test of earlier results and brings notable change to key groups, especially in rosids, while substantiating many previously predicted relationships. Scaling this tree to time using 200 fossils, we discovered that early angiosperm evolution was characterized by high gene tree conflict and explosive diversification, giving rise to more than 80% of extant angiosperm orders. Steady diversification ensued through the remaining Mesozoic Era until rates resurged in the Cenozoic Era, concurrent with decreasing global temperatures and tightly linked with gene tree conflict. Taken together, our extensive sampling combined with advanced phylogenomic methods shows the deep history and full complexity in the evolution of a megadiverse clade

Complex evolutionary history of two ecologically significant grass genera, Themeda and Heteropogon (Poaceae: Panicoideae: Andropogoneae)

Themeda and Heteropogon are closely related grass genera frequently dominant in tropical C4 grasslands. Relationships between them are poorly resolved, impeding ecological study, especially of T. triandra with a broad distribution from Africa to East Asia, and H. contortus with a pantropical distribution. Our analyses of plastome and nuclear genomes with comprehensive sampling of Themeda and Heteropogon demonstrate that neither genus is monophyletic as currently circumscribed. Plastome and nuclear data place H. melanocarpus and H. ritchiei in Themeda. Nested in T. triandra are T. quadrivalvis and T. unica, demonstrating that this widespread species is more morphologically diverse than previously recognized. Heteropogon fischerianus is nested in H. contortus. The picture is more complex for H. triticeus that is sister to H. contortus in the nuclear analysis and to Cymbopogon in the plastome analysis. This incongruence between nuclear and plastid phylogenetic trees suggests hybridization between Cymbopogon-related genome donors and H. contortus. Plastome dating estimates the Themeda–Heteropogon crown age at c. 7.6 Myr, consistent with the Miocene C4 grassland expansion. Themeda triandra and H. contortus diversified 1–2 Mya in the Pleistocene. These results establish a foundation for studying the history of these ecologically significant widespread grasses and the ecosystems they form

A Computation Model for Z Based On Concurrent Constraint Resolution

. We present a computation model for Z, which is based on a reduction to a small calculus, called Z, and on concurrent constraint resolution techniques applied for computing in this calculus. The power of the model is comparable to that of functional logic languages, and combines the strength of higher-order functional computation with logic computation. The model is implemented as part of the ZETA system, where it is used for executing Z specifications for the purpose of test-data evaluation and prototyping. 1 Introduction The automatic evaluation of test data for safety-critical systems is an interesting application that can help to put formal methods into industrial practice. Some studies report that more than 50% of development costs in this application area go into testing. A setting for test-case evaluation that can improve this situation is as follows: given a requirements specification, some input data describing a test case, and the output data from a run of the system's impl..