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Chloridoideae (chloridoid grasses) are a subfamily of ca. 1700 species with high diversity in arid habitats. Until now, their evolutionary relationships have primarily been studied with DNA sequences from the chloroplast, a maternally inherited organelle. Next-generation sequencing is able to efficiently recover large numbers of nuclear loci that can then be used to estimate the species phylogeny based upon bi-parentally inherited data. We sought to test our chloroplast-based hypotheses of relationships among chloridoid species with 122 nuclear loci generated through targeted-enrichment next-generation sequencing, sometimes referred to as hyb-seq. We targeted putative single-copy housekeeping genes, as well as genes that have been implicated in traits characteristic of, or particularly labile in, chloridoids: e.g., drought and salt tolerance. We recovered ca. 70% of the targeted loci (122 of 177 loci) in all 47 species sequenced using hyb-seq. We then analyzed the nuclear loci with Bayesian and coalescent methods and the resulting phylogeny resolves relationships between the four chloridoid tribes. Several novel findings with this data were: the sister lineage to Chloridoideae is unresolved; Centropodia+Ellisochloa are excluded from Chloridoideae in phylogenetic estimates using a coalescent model; Sporobolus subtilis is more closely related to Eragrostis than to other species of Sporobolus; and Tragus is more closely related to Chloris and relatives than to a lineage of mainly New World species. Relationships in Cynodonteae in the nuclear phylogeny are quite different from chloroplast estimates, but were not robust to changes in the method of phylogenetic analysis. We tested the data signal with several partition schemes, a concatenation analysis, and tests of alternative hypotheses to assess our confidence in this new, nuclear estimate of evolutionary relationships. Our work provides markers and a framework for additional phylogenetic studies that sample more densely within chloridoid tribes. These results represent progress towards a robust classification of this important subfamily of grasses, as well as proof-of-concept for hyb-seq next-generation sequencing as a method to generate sequences for phylogenetic analyses in grasses and other plant families., (Copyright © 2016 Elsevier Inc. All rights reserved.)

Background and Aims Few studies of angiosperms have focused on androecial evolution in conjunction with evolutionary shifts in corolla morphology and pollinator relationships. The Western Hemisphere clade of Justiciinae (Acanthaceae) presents the rare opportunity to examine remarkable diversity in staminal morphology. We took a phylogenetically informed approach to examine staminal diversity in this hypervariable group and asked whether differences in anther thecae separation is associated with phylogenetically informed patterns of variation in corolla morphology. We further discuss evidence for associations between anther diversity and pollinators in this lineage. Methods For the Dianthera / Sarotheca / Plagiacanthus (DSP) clade of Western Hemisphere Justiciinae, we characterized floral diversity based on a series of corolla measurements and using a model-based clustering approach. We then tested for correlations between anther thecae separation and corolla traits, and for shifts in trait evolution, including evidence for convergence. Key Results There is evolutionary vagility in corolla and anther traits across the DSP clade with little signal of phylogenetic constraint. Floral morphology clusters into four distinct groups that are, in turn, strongly associated with anther thecae separation, a novel result in Acanthaceae and, to our knowledge, across flowering plants. These cluster groups are marked by floral traits that strongly point to associations with pollinating animals. Specifically, species that are known or likely to be hummingbird pollinated have stamens with parallel thecae, whereas those that are likely bee or fly pollinated have stamens with offset, divergent thecae. Conclusions Our results suggest that anther thecae separation is likely under selection in concert with other corolla characters. Significant morphological shifts detected by our analyses corresponded to putative shifts from insect to hummingbird pollination. Results from this study support the hypothesis that floral structures function in an integrated manner and are likely subject to selection as a suite. Further, these changes can be hypothesized to represent adaptive evolution. [ABSTRACT FROM AUTHOR]

Premise of research. Plants with C4 photosynthesis are able to produce carbohydrates more efficiently than plants with C3 photosynthesis in warm climates when levels of atmospheric CO2 are reduced. The C4 pathway has evolved multiple times in distantly related lineages, but it is not known whether the same physiological transitions occurred in all lineages. Species with intermediate C3-C4 physiology and anatomy offer the opportunity to study how plants transition from C3 to C4. It is thus vital to characterize phylogenetic relationships and photosynthetic pathways in groups with C3-C4 intermediate species, as well as C3 and C4 species. Methodology. We assessed photosynthetic pathway evolution in the Afro-Asian genus Blepharis (Acanthaceae) by sampling 99 species for carbon isotope ratios, 18 species for leaf anatomy, and 36 species for phylogenetic analysis. We estimated when Blepharis clades diverged using a BEAST molecular dating analysis, and we estimated ancestral distributions using BioGeoBEARS. We also estimated ancestral photosynthetic pathways in Blepharis, along with the rate of transitions between C3, C3-C4 intermediates, and C4 photosynthesis. Finally, we analyzed the climatic niches of 93 Blepharis taxa to better understand the current distribution patterns of species with different photosynthetic pathways. Pivotal results. Of the 99 species of Blepharis sampled for carbon isotope ratios, 13 are C4, 2 are C4-like, and 84 have values that indicate that they use a C3 cycle. Nine species are putative C3-C4 intermediate species based on leaf anatomy. All of the C4 and C3-C4 intermediate species are in section Acanthodium and are closely related. Our estimates suggest that C4 photosynthesis evolved two or three times in southern Africa and Asia between 1 and 5 million years ago. Conclusions. We present a phylogenetic framework of Blepharis and hypotheses of where and when C4 photosynthesis evolved in the genus. There are more than 40 species in section Acanthodium that are not C4, some of which may be C3-C4 intermediate species. Blepharis thus contains many candidate C3-C4 intermediate species and provides an opportunity for detailed comparative analyses of the evolution of photosynthetic pathways. [ABSTRACT FROM AUTHOR]