We present a new worldwide phylogenetic classification of 11506 grass species in 768 genera, 12 subfamilies, seven supertribes, 52 tribes, five supersubtribes, and 90 subtribes; and compare two phylogenetic classifications of the grass family published in 2015 (Soreng et al. and Kellogg). The subfamilies (in descending order based on the number of species) are Pooideae with 3968 species in 202 genera, 15 tribes, and 30 subtribes; Panicoideae with 3241 species in 247 genera, 13 tribes, and 19 subtribes; Bambusoideae with 1670 species in 125 genera, three tribes, and 15 subtribes; Chloridoideae with 1602 species in 124 genera, five tribes, and 26 subtribes; Aristidoideae with 367 species in three genera, and one tribe; Danthonioideae with 292 species in 19 genera, and one tribe; Micrairoideae with 184 species in eight genera, and three tribes; Oryzoideae with 115 species in 19 genera, four tribes, and two subtribes; Arundinoideae with 40 species in 14 genera, two tribes, and two subtribes; Pharoideae with 12 species in three genera, and one tribe; Puelioideae with 11 species in two genera, and two tribes; and the Anomochlooideae with four species in two genera, and two tribes. We also include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. Newly described taxa include: supertribes Melicodae and Nardodae; supersubtribes Agrostidodinae, Boutelouodinae, Gouiniodinae, Loliodinae, and Poodinae; and subtribes Echinopogoninae and Ventenatinae.

A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications

https://www.cell.com/trends/plant-science/pdf/S1360-1385(15)00176-4.pdf

Genome skimming for next-generation biodiversity analysis.

The systematics of grasses has advanced through applications of plastome phylogenomics, although studies have been largely limited to subfamilies or other subgroups of Poaceae Here we present a plastome phylogenomic analysis of 250 complete plastomes (179 genera) sampled from 44 of the 52 tribes of Poaceae Plastome sequences were determined from high throughput sequencing libraries and the assemblies represent over 287 Mbases of sequence data Phylogenetic signal was characterized in 14 partitions, including (1) complete plastomes; (2) protein coding regions; (3) noncoding regions; and (4) three loci commonly used in single and multi-gene studies of grasses Each of the four main partitions was further refined, alternatively including or excluding positively selected codons and also the gaps introduced by the alignment All 76 protein coding plastome loci were found to be predominantly under purifying selection, but specific codons were found to be under positive selection in 65 loci The loci that have been widely used in multi-gene phylogenetic studies had among the highest proportions of positively selected codons, suggesting caution in the interpretation of these earlier results Plastome phylogenomic analyses confirmed the backbone topology for Poaceae with maximum bootstrap support (BP) Among the 14 analyses, 82 clades out of 309 resolved were maximally supported in all trees Analyses of newly sequenced plastomes were in agreement with current classifications Five of seven partitions in which alignment gaps were removed retrieved Panicoideae as sister to the remaining PACMAD subfamilies Alternative topologies were recovered in trees from partitions that included alignment gaps This suggests that ambiguities in aligning these uncertain regions might introduce a false signal Resolution of these and other critical branch points in the phylogeny of Poaceae will help to better understand the selective forces that drove the radiation of the BOP and PACMAD clades comprising more than 999% of grass diversity

A 250 plastome phylogeny of the grass family (Poaceae): topological support under different data partitions

Whole genome sequencing is helping generate robust phylogenetic hypotheses for a range of taxonomic groups that were previously recalcitrant to classical molecular phylogenetic approaches. As a case study, we performed a shallow shotgun sequencing of eight species in the tropical tree family Chrysobalanaceae to retrieve large fragments of high-copy number DNA regions and test the potential of these regions for phylogeny reconstruction. We were able to assemble the nuclear ribosomal cluster (nrDNA), the complete plastid genome (ptDNA) and a large fraction of the mitochondrial genome (mtDNA) with approximately 1000×, 450× and 120× sequencing depth respectively. The phylogenetic tree obtained with ptDNA resolved five of the seven internal nodes. In contrast, the tree obtained with mtDNA and nrDNA data were largely unresolved. This study demonstrates that genome skimming is a cost-effective approach and shows potential in plant molecular systematics within Chrysobalanaceae and other under-studied groups.

Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family

C4 photosynthesis is a complex physiological adaptation that confers greater productivity than the ancestral C3 photosynthetic type in environments where photorespiration is high. It evolved in multiple lineages through the coordination of anatomical and biochemical components, which concentrate CO2 at the active site of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco). In most C4 plants, the CO2-concentrating mechanism is achieved via the confinement of Rubisco to bundle-sheath cells, into which CO2 is biochemically pumped from surrounding mesophyll cells. The C4 biochemical pathway relies on a specific suite of leaf functional properties, often referred to as Kranz anatomy. These include the existence of discrete compartments differentially connected to the atmosphere, a close contact between these compartments, and a relatively large compartment to host the Calvin cycle. In this review, we use a quantitative dataset for grasses (Poaceae) and examples from other groups to isolate the changes in anatomical characteristics that generate these functional properties, including changes in the size, number, and distribution of different cell types. These underlying anatomical characteristics vary among C4 origins, as similar functions emerged via different modifications of anatomical characteristics. In addition, the quantitative characteristics of leaves all vary continuously across C3 and C4 taxa, resulting in C4-like values in some C3 taxa. These observations suggest that the evolution of C4-suitable anatomy might require relatively few changes in plant lineages with anatomical predispositions. Furthermore, the distribution of anatomical traits across C3 and C4 taxa has important implications for the functional diversity observed among C4 lineages and for the approaches used to identify genetic determinants of C4 anatomy.

/pdf/deconstructing-kranz-anatomy-to-understand-c4-evolution-55xd2zmod8.pdf

Deconstructing Kranz anatomy to understand C4 evolution

Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar.

\n Debates regarding the origin of tropical savannas have attempted to disentangle the role of human, biotic and abiotic factors. Understanding the origins of savanna remains essential to identifying processes that gave rise to habitat mosaics, particularly those found in the Central Plateau of Madagascar. Documenting the evolutionary history and demography of native trees occurring in open habitats may reveal footprints left by past and recent environmental changes. We conducted a population genetic analysis of an endangered Malagasy shrub (Noronhia lowryi, Oleaceae) of the Central Plateau. Seventy-seven individuals were sampled from three sites and genotyped at 14 nuclear and 24 chloroplast microsatellites. We found a highly contrasting nuclear and plastid genetic structure, suggesting that pollen-mediated gene flow allows panmixia, while seed-based dispersal may rarely exceed tens of metres. From a phylogeny based on full plastomes, we dated the surprisingly old crown age of maternal lineages back to ~6.2 Mya, perhaps co-occurring with the global expansion of savanna. In contrast, recent demographic history inferred from nuclear data shows a bottleneck signature ~350 generations ago, probably reflecting an environmental shift during the Late Pleistocene or the Holocene. Ancient in situ adaptation and recent demographic collapse of an endangered woody plant highlight the unique value and vulnerability of the Malagasy savannas.

Hélène Ralimanana

Papers

Phylogenomics and taxonomy of Lecomtelleae (Poaceae), an isolated panicoid lineage from Madagascar.

Late Miocene origin and recent population collapse of the Malagasy savanna olive tree (Noronhia lowryi)