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Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tools.

The taxonomy of the tribe Fabeae (Vicieae) has long been problematic, but an analysis by Schaefer et al. in 2012 gave an exceptionally clear view of the tribe and noted the possibility that some nomenclatural adjustments may be required at some future date. These authors suggested several options, expressing some preferences. However, there has been a recent change to formally accepted names, implementing one of these possibilities, but without any additional relevant information. This change seems unjustified and unhelpful. We therefore present an argument for the retention, or re-instatement, of the genera Pisum, Vavilovia, and Lens until such time as new data support this requirement and there is no nomenclatural solution that is both accurate and convenient. [ABSTRACT FROM AUTHOR]

Ulmaceae is a woody family widespread in northern temperate forests. Despite the ecological importance of this family, its phylogeny and biogeographic history are poorly understood. In this study, we reconstruct phylogenetic relationships within the family and infer spatio‐temporal diversification patterns based on chloroplast genome (complete cpDNA) and nuclear ribosomal DNA sequences (nrDNA). The seven Ulmaceae genera are resolved in two main clades (temperate vs. tropical) by both cpDNA and nrDNA sequences. The temperate clade includes four genera, Hemiptelea, Zelkova, Planera, and Ulmus. The relationships among Planera and other genera are controversial because of inconsistent topologies between plastid and nuclear data. The tropical clade includes three genera ((Ampelocera, Phyllostylon), Holoptelea). Molecular dating and diversification analyses show that Ulmaceae originated in the Early Cretaceous (ca. 110–125 Ma) with the main lineages establishing from the Late Cretaceous to the early Eocene. The diversification rate slowed during the middle to the late Paleogene (ca. 23–45 Ma), followed by a rapid diversification of the East Asian temperate group in the Neogene, congruent with a global cooling event. The ancestral state optimization analysis suggests an East Asian origin of the temperate Ulmaceae clade during the Paleocene, which is consistent with the fossil record. Both phylogenomic and fossil evidence support East Asia as a center of origin and diversification for the temperate woody lineages. [ABSTRACT FROM AUTHOR]

Mountains are often more species-rich than lowlands. This could be the result of migration from lowlands to mountains, of a greater survival rate in mountains, or of a higher diversification rate in mountains. We investigated this question in the globally distributed family Ericaceae, which includes c. 4426 species ranging from sea level to > 5000 m. We predict that the interaction of low specific leaf area ( SLA) and montane habitats is correlated with increased diversification rates., A molecular phylogeny of Ericaceae based on rbcL and matK sequence data was built and dated with 18 fossil calibrations and divergence time estimates. We identified radiations using bamm and correlates of diversification rate changes using binary-state speciation and extinction (Bi SSE) and multiple-state speciation and extinction (Mu SSE) analyses., Analyses revealed six largely montane radiations. Lineages in mountains diversified faster than nonmountain lineages (higher speciation rate, but no difference in extinction rate), and lineages with low SLA diversified faster than high- SLA lineages. Further, habitat and trait had a positive interactive effect on diversification., Our results suggest that the species richness in mountains is the result of increased speciation rather than reduced extinction or increased immigration. Increased speciation in Ericaceae was facilitated by low SLA. [ABSTRACT FROM AUTHOR]

* Premise of the study: The radiation of a lineage and its rise to ecological dominance are distinct phenomena and driven by different processes. For example, paleoecological data has been used to show that the Cretaceous angiosperm radiation did not coincide with their rise to dominance. Using a phylogenetic approach, we here explored the evolution of C4 grasses and evaluated whether the diversification of this group and its rise to ecological dominance in the late Miocene were decoupled. * Methods: We assembled a matrix including 675 grass species of the PACMAD clade and 2784 characters (ITS and ndhF) to run a molecular dating analysis using three fossils as reference calibrations. We coded species as C3 vs. C4 and reconstructed ancestral states under maximum likelihood. We used the program BiSSE to test whether rates of diversification are correlated with photosynthetic pathway and whether the radiation of C4 lineages preceded or coincided with their rise to ecological dominance from -10 Ma. * Key results: C4 grass lineages first originated around 35 Ma at the time of the Eocene-Oligocene transition. Accelerated diversification of C4 lineages did not coincide with their rise to ecological dominance. * Conclusions: C4-dominated grasslands have expanded only since the Late Miocene and Pliocene. The initial diversification of their biotic elements can be tracked back as far as the Eocene-Oligocene transition. We suggest that shifts in taxonomic diversification and ecological dominance were stimulated by different factors, as in the case of the early angiosperms in the Cretaceous. [ABSTRACT FROM AUTHOR]

C4 grasses constitute the main component of savannas and are pervasive in other dry tropical ecosystems where they serve as the main diet for grazing animals. Among potential factors driving C4 evolution of grasses, the interaction between grasses and grazers has not been investigated. To evaluate if increased grazing pressure may have selected for higher leaf silica production as the grasses diverged, we reconstructed the phylogeny of all 800 genera of the grass family with both molecular (combined multiplastid DNA regions) and morphological characters. Using molecular clocks, we also calculated the age and number of origins of C4 clades and found that shifts from C3 to C4 photosynthesis occurred at least 12 times starting 30.9 million years ago and found evidence that the most severe drop in atmospheric carbon dioxide in the late Oligocene (between 33 and 30 million years ago) matches the first origin of C4 photosynthesis in Chloridoideae. By combining fossil and phylogenetic data for ungulates and implementing a randomization procedure, our results showed that the appearance of C4 grass clades and ungulate adaptations to C4-dominated habitats match significantly in time. An increase of leaf epidermal density of silica bodies was found to correspond to postulated shifts in diversification rates in the late Miocene [24 significant shifts in diversification ( P<0.05) were detected between 23 and 3.7 million years ago]. For aristidoid and chloridoid grasses, increased grazing pressure may have selected for a higher leaf epidermal silica production in the late Miocene. [ABSTRACT FROM AUTHOR]

In the most comprehensive study to date we explored the phylogeny and evolution of the genus Asparagus , with emphasis on the southern African species. We included 211 accessions, representing 77 (92%) of the southern African, 6 (17%) of the tropical African, 10 (56%) of the strictly European and 6 (9%) of the Eurasian species. We analyzed DNA sequences from three plastid regions ( trn H- psb A, trn D-T, ndh F) and from the nuclear region phytochrome C (PHYC) with parsimony and maximum likelihood methods, and recovered a monophyletic Asparagus . The phylogeny conflicts with all previous infra-generic classifications. It has many strongly supported clades, corroborated by morphological characters, which may provide a basis for a revised taxonomy. Additionally, the phylogeny indicates that many of the current species delimitations are problematic. Using biogeographic analyses that account for phylogenetic uncertainty (S-DIVA) and take into account relative branch lengths (Lagrange) we confirm the origin of Asparagus in southern Africa, and find no evidence that the dispersal of Asparagus follow the Rand flora pattern. We find that all truly dioecious species of Asparagus share a common origin, but that sexual dimorphism has arisen independently several times. [ABSTRACT FROM AUTHOR]