Liliana M. Giussani

A molecular phylogeny of the grass subfamily Panicoideae (Poaceae) shows multiple origins of C4 photosynthesis

DNA sequence data from the chloroplast gene ndhF were analyzed to estimate the phylogeny of the subfamily Panicoideae, with emphasis on the tribe Paniceae. Our data suggest that the subfamily is divided into three strongly supported clades, corresponding to groups with largely identical base chromosome numbers. Relationships among the three clades are unclear. In unweighted parsimony analyses, the two major clades with x = 10 (Andropogoneae and x = 10 Paniceae) are weakly supported as sister taxa. The third large clade corresponds to x = 9 Paniceae. In analyses under implied weight, the two clades of Paniceae are sisters, making the tribe monophyletic. Neither resolution is strongly supported.Our molecular phylogenies are not congruent with previous classifications of tribes or subtribes. Based on this sample of species, we infer that C(4) photosynthesis has evolved independently several times, although a single origin with multiple reversals and several reacquisitions is only slightly less parsimonious. The phosphoenol pyruvate carboxykinase (PCK) subtype of C(4) photosynthesis has evolved only once, as has the NAD-malic enzyme (ME) subtype; all other origins are NADP-ME. Inflorescence bristles are apparently homologous in the genera Setaria and Pennisetum, contrary to opinions of most previous authors. Some genera, such as Digitaria, Echinochloa, and Homolepis are supported as monophyletic. The large genus Paspalum is shown to be paraphyletic, with Thrasya derived from within it. As expected, Panicum is polyphyletic, with lineages derived from multiple ancestors across the tree. Panicum subg. Panicum is monophyletic. Panicum subg. Dichanthelium, subg. Agrostoides, and subg. Phanopyrum are unrelated to each other, and none is monophyletic. Only Panicum subg. Dichanthelium sect. Dichanthelium, represented by P. sabulorum and P. koolauense, is monophyletic. Panicum subg. Megathyrsus, a monotypic subgenus including only the species P. maximum, is better placed in Urochloa, as suggested by other authors.

A molecular phylogeny of Panicum (Poaceae: Paniceae): tests of monophyly and phylogenetic placement within the Panicoideae.

Panicum L. is a cosmopolitan genus with approximately 450 species. Although the genus has been considerably reduced in species number with the segregation of many taxa to independent genera in the last two centuries, Panicum remains a heterogeneous assemblage, as has been demonstrated in recent years. The genus is remarkably uniform in its floral characters but exhibits considerable variation in anatomical, physiological, and cytological features. As a result, several classifications, and criteria of what the genus should really include, have been postulated in modern literature. The purpose of this research, based on molecular data of the chloroplast ndhF gene, is to test the monophyly of Panicum, to evaluate infrageneric classifications, and to propose a robust phylogenetic hypothesis. Based on the present results, previous morphological and molecular phylogenetic studies, and inferred diagnostic morphological characters, we restrict Panicum sensu stricto (s.s.) to the former subgenus Panicum and support recognition of Dichanthelium, Phanopyrum, and Steinchisma as distinct genera. We have transfered other species of Panicum to other genera of the Paniceae. Most of the necessary combinations have been made previously, so few nomenclatural changes have been required. The remaining species of Panicum sensu lato (s.l.) are included within Panicum incertae sedis representing isolated species or species grouped within monophyletic clades. Additionally, we explore the performance of the three codon position characters in producing the supported phylogeny.

Phylogeny of the Paniceae (Poaceae: Panicoideae): integrating plastid DNA sequences and morphology into a new classification

Included in the PACMAD clade of the family Poaceae (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae), the tribe Paniceae s.l. is one of the largest tribes of the subfamily Panicoideae, with more than 2000 species. This tribe comprises a huge morphological, cytological and physiological diversity represented by different inflorescence types, several basic chromosome numbers, and at least four major photosynthetic pathways. The tribe Paniceae has been the subject of molecular studies that have confirmed its paraphyly: two major clades were recognized based on their basic chromosome numbers (x = 9, x = 10). The x = 10 Paniceae clade is sister to the Andropogoneae–Arundinelleae s.s. clade (x = 10), while the combined x = 10 clade is sister to the x = 9 clade that contains the remaining genera of Paniceae. As a result of a recent realignment within the tribe in terms of the phylogenetic position of minor and major Paniceae genera, a reanalysis of the whole sampling is performed and new underrepresented taxa are discussed. A total of 155 genera, currently considered within subfamily Panicoideae, are represented here by almost all genera of Paniceae s.l., representatives of Andropogoneae and Arundinelleae s.s., and the endemic and small tribe Steyermarkochloeae; we also included specimens of subfamily Micrairoideae, tribes Isachneae and Eriachneae. The sampling includes as outgroups 18 genera of the PACMAD clade (excluding Panicoideae) and four genera from the BEP clade (Bambusoideae, Ehrhartoideae, Pooideae), rooting with Bromus inermis. A matrix with 265 taxa based on the combined evidence from ndhF plastid sequences (2074 bp) and 57 morphological characters was subjected to parsimony analyses. Jackknife resampling was used to calculate group support. Most clades are characterized by morphological, cytological, anatomical, and/or physiological characters. Major tribal changes are based on the basic chromosome number; the pantropical x = 9 clade is here recognized as Paniceae s.s., while the American x = 10 Paniceae s.l. is restricted to the reinstated tribe Paspaleae. The optimization of the photosynthetic pathway for the Paspaleae–Andropogoneae–Arundinelleae s.s. clade, including the monotypic Reynaudia, shows a plesiomorphic C4 state while the ancestral state for Paniceae s.s. is ambiguous. If Reynaudia were not included or placed elsewhere, the ancestral photosynthetic pathway for both the Paspaleae–Andropogoneae–Arundinelleae s.s. clade and the Paniceae s.s. would be unambiguously C3. In order to explore character evolution further, the morphological characters were mapped onto one of the most parsimonious trees. A relationship between photosynthetic pathways and inflorescence morphology is suggested here for the first time. Based on the optimization of morphological characters and additional data, we propose names for almost all inner clades at the rank of subtribe with a few groups as incertae sedis. With this extensive sampling, we resolved the phylogenetic relationships and the assignation of synapomorphies, and improved the support in subtribe sorting; consequently a robust circumscription of the tribe Paniceae s.l. is proposed.

Phylogenetic studies favour the unification of Pennisetum, Cenchrus and Odontelytrum (Poaceae): a combined nuclear, plastid and morphological analysis, and nomenclatural combinations in Cenchrus

BACKGROUNDS AND AIMS Twenty-five genera having sterile inflorescence branches were recognized as the bristle clade within the x = 9 Paniceae (Panicoideae). Within the bristle clade, taxonomic circumscription of Cenchrus (20-25 species), Pennisetum (80-140) and the monotypic Odontelytrum is still unclear. Several criteria have been applied to characterize Cenchrus and Pennisetum, but none of these has proved satisfactory as the diagnostic characters, such as fusion of bristles in the inflorescences, show continuous variation. METHODS A phylogenetic analysis based on morphological, plastid (trnL-F, ndhF) and nuclear (knotted) data is presented for a representative species sampling of the genera. All analyses were conducted under parsimony, using heuristic searches with TBR branch swapping. Branch support was assessed with parsimony jackknifing. KEY RESULTS Based on plastid and morphological data, Pennisetum, Cenchrus and Odontelytrum were supported as a monophyletic group: the PCO clade. Only one section of Pennisetum (Brevivalvula) was supported as monophyletic. The position of P. lanatum differed among data partitions, although the combined plastid and morphology and nuclear analyses showed this species to be a member of the PCO clade. The basic chromosome number x = 9 was found to be plesiomorphic, and x = 5, 7, 8, 10 and 17 were derived states. The nuclear phylogenetic analysis revealed a reticulate pattern of relationships among Pennisetum and Cenchrus, suggesting that there are at least three different genomes. Because apomixis can be transferred among species through hybridization, its history most likely reflects crossing relationships, rather than multiple independent appearances. CONCLUSIONS Due to the consistency between the present results and different phylogenetic hypotheses (including morphological, developmental and multilocus approaches), and the high support found for the PCO clade, also including the type species of the three genera, we propose unification of Pennisetum, Cenchrus and Odontelytrum. Species of Pennisetum and Odontelytrum are here transferred into Cenchrus, which has priority. Sixty-six new combinations are made here.

Phylogenetic Studies in the Paniceae (Poaceae) : a Realignment of Section Lorea of Panicum

Abstract The taxonomic status of Panicum section Lorea has remained as “incertae sedis” within Panicum. To resolve its position within the Paniceae and to test the monophyly of this section, phylogenetic analyses based on chloroplast sequence data (ndhF) and morphology were conducted for the Paniceae with particular emphasis on Panicum section Lorea. The results did not support the monophyly of this section. The species of this group were resolved in two clades which are not sister groups and neither of them is closely related to Panicum s.s. As a result, two new genera are proposed and described: Apochloa and Renvoizea, which are restricted to the Guiana highlands and eastern Brazil. New combinations are: Apochloa animara, A. bahiense, A. chnoodes, A. cipoense, A. eligulata, A. euprepes, A. jauana, A. lorea, A. lutzii, A. molinioides, A. poliophylla, A. sipapoense, A. steyermarkii, A. subtiramulosa, A. tijucae, Renvoizea acicularifolia, R. durifolia, R. glaziovii, R. lagostachya, R. marauense, R. restingae, R. sacciolepoides, R. teretifolia, R. trinii, and R. vaginiviscosa.

Molecular phylogeny of the subtribe Melinidinae (Poaceae: Panicoideae: Paniceae) and evolutionary trends in the homogenization of inflorescences

The subtribe Melinidinae (Poaceae: Panicoideae: Paniceae) includes 14 genera that present the PCK photosynthetic subtype in addition to several other unique and also common characters. The purpose of this research was (1) to test the monophyly of the subtribe Melinidinae, including 331 ndhF sequences of Panicoids and related genera, (2) to analyze the phylogenetic relationships among genera of Melinidinae using four cpDNA regions, and (3) to study evolutionary trends in the homogenization of inflorescences. As a result, the monophyly of Melinidinae is supported if Urochloa venosa is excluded from the subtribe. Alloteropsis semialata subsp. semialata, an unusual PCK species, is here confirmed within the Forest shade clade. Within Melinidinae, Urochloa and Eriochloa appeared as paraphyletic and polyphyletic genera, respectively. Finally, the general trend in the evolution of the inflorescences in Melinidinae seems to be the reduction from non-homogenized to complete homogenized inflorescences.

A Phylogeny of Piptochaetium (Poaceae: Pooideae: Stipeae) and Related Genera Based on a Combined Analysis Including Trnl-f, Rpl16, and Morphology

Abstract The tribe Stipeae occurs in temperate and warm temperate grasslands of Eurasia, Australia, and America. Although generic circumscription within the tribe has recently undergone significant changes, the American genus Piptochaetium has been clearly defined by morphological and anatomical characters. It includes 36 species and 2 varieties, most of them widely distributed in temperate grasslands of South America. Phylogenetic analyses were conducted in Piptochaetium and allied genera of the Stipeae, in order to test the monophyly of the genus, re-examine infrageneric taxa, and analyze relationships among species of this genus and allied genera of Stipeae. Two chloroplast molecular markers, trnL-F and rpl16, as well as morphology were used. Topology between morphological and molecular data mainly differs in the relationships of Piptochaetium with Anatherostipa and Piptatherum. Molecular and combined analyses yielded two major clades in the tribe: the x  =  11 Clade with Piptochaetium, Aciachne, Anatherostipa, and Jarava vaginata, and the Aneuploid Clade with Jarava, Nassella, and Piptatherum. Monophyly of Piptochaetium was confirmed by morphological and total evidence (morphology and DNA data) analyses. Monophyly of sect. Podopogon, sect. Piptochaetium and Nassella were only supported by the total evidence analysis. Circumscription of Jarava is also discussed.

Phylogenetic Relationships in the Genus Paspalum (Poaceae: Panicoideae: Paniceae): an Assessment of the Quadrifaria and Virgata Informal Groups

Abstract Paspalum, an American genus of the x = 10 Paniceae clade, includes about 330 species, four subgenera, and 27 informal groups. Within the genus, the Quadrifaria and Virgata groups are well-represented in South and Central America. Interspecific variability make the delimitation of these groups difficult; hence several species have been included or excluded from Quadrifaria or Virgata depending on the taxonomic treatment. In previous analyses, the Quadrifaria and Virgata groups of Paspalum were polyphyletic. Here we present a new appraisal of the classification of both groups based on the phylogenetic analyses of DNA data from the chloroplast: the rpl16 intron, and the region comprising the trnL and trnF genes. A monophyletic Virgata clade is recovered, consisting of nearly all the species listed in an unpublished manuscript. The Quadrifaria group is restricted to P. quadrifarium and P. quarinii. Other clades grouped species traditionally treated within Virgata or Quadrifaria, although their phylogenetic placement needs to be reevaluated. Within most of the clades, diploid and polyploid species seemingly derive from a common ancestor denoting an autopolyploid origin. Alloploidy is also possible although reticulate evolution needs to be explored. The wide distribution of the I genome suggests that this is a plesiomorphic state in Paspalum.

Phylogeny of New World Stipeae (Poaceae): an evaluation of the monophyly of Aciachne and Amelichloa

© The Willi Hennig Society 2010.

On the taxonomic position of Panicum aristellum (Poaceae: Panicoideae: Paniceae)

Abstract In a recent treatment, the genus Panicum was restricted to subgenus Panicum based on molecular, morphological, and anatomical data. Also, other species of Panicum were transferred to different genera of the Paniceae, such as Dichanthelium, Hymenachne, Phanopyrum, and Steinchisma, while the remaining American species of Panicum were temporarily placed as incertae sedis taxa. Therefore, these incertae sedis species are in need of a new taxonomic status within the tribe. In this study, the taxonomic position of Panicum aristellum, an endemic species of central and southeastern Brazil, is evaluated using morphological and anatomical characters, together with sequence data from ndhF, a molecular marker from the chloroplast. The sequence of Panicum aristellum was analyzed together with other species of the subfamily Panicoideae. This species grouped with the genus Canastra in a well-supported clade. Several synapomorphies characterized the clade: caespitose plants, keeled sheaths, aristate spikelets, scabrous bracts, the number of nerves of the glumes and lower lemma, the presence of a lower palea and lower flower, a non-indurate upper anthecium, and a similar geographical distribution. In addition, both species are C3 with non-Kranz anatomy. As a result, the new combination Canastra aristella is proposed and the species is compared to putatively related genera within the Paniceae.