Genomic, karyological and morphological changes of South American garlics (Ipheion) provide insights into mechanisms of speciation in the Pampean region

Speciation proceeds through mechanisms that promote reproductive isolation and shape the extent of genetic variation in natural populations, and thus its study is essential to understand the evolutionary processes leading to increased biodiversity. Chromosomal rearrangements are known to facilitate reproductive isolation by hybrid sterility and favour speciation events. The genus Ipheion (Amaryllidaceae, Allioideae) is unique as its species exhibit a remarkable karyological variability but lack population-level genetic data. To unveil the diversification processes acting upon the formation of new lineages within Ipheion in the Pampas of South America, we combined morphology and karyology approaches with genotyping-by-sequencing. Our phylogenomic and population genomics results supported the taxonomic division of Ipheion into three morphological and genetically well-differentiated groups. The origin of Ipheion uniflorum was traced back to its current southern distribution area in the southern Pampean region (in Argentina), from where it had expanded to the north reaching Uruguay. Our results further suggested that chromosome rearrangements and ploidy shifts had triggered speciation events, first during the origin of I. uniflorum and later during its subsequent diversification into I. recurvifolium and I. tweedieanum, in both cases reinforced by extrinsic factors and biogeographical settings. The current study illustrates the analytical power of multidisciplinary approaches integrating phylo- and population genomics with classic analyses to reveal evolutionary processes in plants.

A novel indicator of karyotype evolution in the tribe Leucocoryneae (Allioideae, Amaryllidaceae)

The tribe Leucocoryneae is taxonomically and cytogenetically complex, mainly due to its extraordinary morphological and karyological variation. Robertsonian translocations had long been recognized as a central factor contributing to karyotype diversity within the Leucocoryneae, but so far no major tendency prevailing on the observed complexity of karyotype formula among species has been identified. The assessment of nuclear DNA contents by flow cytometry using propidium iodide in 23 species, representing all genera within the tribe, showed a monoploid genome size variation of 1Cx = 9.07-30.46 pg denoting a threefolds fluctuation. A highly significant linear association between the average DNA content per chromosome arm (2C/FN) and the monoploid genome size (1Cx) is reported for the first time and identified as a novel indicator of a trend governing karyotype diversity within Leucocoryneae. This trend shows that a reduction in DNA content per chromosome arm is influencing and has shaped karyotype evolution of different monophyletic groups within the tribe despite the complex karyotype diversity and apparently contrasting patterns of genome sizes.

Breeding system diversification and evolution in American Poa supersect. Homalopoa (Poaceae: Poeae: Poinae)

BACKGROUND AND AIMS

Poa subgenus Poa supersect. Homalopoa has diversified extensively in the Americas. Over half of the species in the supersection are diclinous; most of these are from the New World, while a few are from South-East Asia. Diclinism in Homalopoa can be divided into three main types: gynomonoecism, gynodioecism and dioecism. Here the sampling of species of New World Homalopoa is expanded to date its origin and diversification in North and South America and examine the evolution and origin of the breeding system diversity.

METHODS

A total of 124 specimens were included in the matrix, of which 89 are species of Poa supersect. Homalopoa sections Acutifoliae, Anthochloa, Brizoides, Dasypoa, Dioicopoa, Dissanthelium, Homalopoa sensu lato (s.l.), Madropoa and Tovarochloa, and the informal Punapoa group. Bayesian and parsimony analyses were conducted on the data sets based on four markers: the nuclear ribosomal internal tanscribed spacer (ITS) and external transcribed spacer (ETS), and plastid trnT-L and trnL-F. Dating analyses were performed on a reduced Poa matrix and enlarged Poaceae outgroup to utilize fossils as calibration points. A relaxed Bayesian molecular clock method was used.

KEY RESULTS

Hermaphroditism appears to be pleisiomorphic in the monophyletic Poa supersect. Homalopoa, which is suggested to have originated in Eurasia 8·4-4·2 million years ago (Mya). The ancestor of Poa supersect. Homalopoa radiated throughout the New World in the Late Miocene-Early Pliocene, with major lineages originating during the Pliocene to Pleistocene (5-2 Mya). Breeding systems are linked to geographic areas, showing an evolutionary pattern associated with different habitats. At least three major pathways from hermaphroditism to diclinism are inferred in New World Homalopoa: two leading to dioecism, one via gynodioecism in South America and another directly from hermaphroditism in North America, a result that needs to be checked with a broader sampling of diclinous species in North America. A third pathway leads from hermaphroditism to gynomonoecism in Andean species of South America, with strictly pistillate species evolving in the highest altitudes.

CONCLUSIONS

Divergence dating provides a temporal context to the evolution of breeding systems in New World Poa supersect. Homalopoa The results are consistent with the infrageneric classification in part; monophyletic sections are confirmed, it is proposed to reclassify species of sect. Acutifoliae, Dasypoa and Homalopoa s.l. and it is acknowledged that revision of the infrageneric taxonomy of the gynomonoecious species is needed.

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.

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.

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.