Miocene–Pliocene speciation, introgression, and migration of Patis and Ptilagrostis (Poaceae: Stipeae)

Insights to the taxonomy and phylogeny of the genus Ptilagrostis worldwide (Poaceae, Stipeae) with a key to species identification, checklist and outlines for further studies

Ptilagrostis (false needlegrass) is a genus of high-mountain grasses distributed in Central and North-East Asia, as well as in North America. The phylogenetic position of the genus Ptilagrostis within the Stipeae is well defined based on micromorphological patterns of lemma epidermis and moleculs. However, there is a lack of a comprehensive taxonomic revision of the genus in its entire distribution range. In this study, we performed comprehensive analyses using integrative taxonomic methods, aiming at both micromorphological and macromorphological analyses, and molecular analyses based on SNPs obtained from DArT genome-wide sequencing, in which we considered all taxa representing the genus in order to establish phylogenetic relationships between its members. We analysed all species possessing the characteristic 'Ptilagrostis pattern' of the lemma epidermis, with a particular reference to species possessing the terminal segment of the awn (seta) covered by short (up to 1 mm long) hairs that, until now, were treated as representatives of the genus Achnatherum. Following with the result of our molecular, morphological and anatomical analyses, the genus Ptilagrostis is represented by 15 species, one subspecies and five varieties organised in three well supported phylogenetic clades corresponding to the three sections: Ptilagrostis, Barkworthia and Chenella. In this paper, we provide an original key to identifying false needlegrass species, together with a checklist containing the intrageneric species-organisation. In addition, for each species, we present the data regarding nomenclatural types, morphological description, and information on the geographical distribution, habitat preferences and altitudinal ranges. We proposed two new varieties within the genus Ptilagrostis, P.glabrifoliavar.himalayensis and P.concinnavar.xizangensis, and the new section Chenella comprising three species with awns scabrous or covered by very short hairs up to 0.3 mm long. Additionally, we transfer Stipachingii to Ptilagrostischingii, Achnatherumchingiivar.laxum to P.chingiivar.laxum, and Ptilagrostisconcinnasubsp.schischkinii to P.junatoviivar.schischkinii. Lectotypification was made for three taxa, Stipamongholicavar.minutiflora, P.czekanowskii, and P.tibetica.

Phylogeography of the neotropical epiphytic orchid, genus Dracula

The tropical Andes constitute a natural barrier between the Pacific Ocean and the Atlantic; in these mountains, are a great variety of Ecosystems, defined by factors such as orography, winds, humidity, temperature, among others. Some of these Ecosystems have different environmental conditions from tropical ones. In them, there is a great Biodiversity, in some cases endemic and associated with relatively small geographic areas. An example of this biodiversity is the orchids of the genus Dracula, about which discussions are currently generated due to the difficulty in classifying their members. The present work shows a study where DNA was isolated and sequenced from plant samples obtained from 52 species of orchids of the genus Dracula, which were analyzed using the MEGA7 software. Phylogenetic analysis of the DNA sequences showed a well-resolved topology that reflects a geographical pattern of several major clades of the Pacific and Atlantic watersheds. Geophysical conditions of the Andes have generated greater biodiversity of the genus Dracula on the side of the Pacific. Although the species Dracula cordobae and alessandroi reported on both sides of the study site belong to the same clade and show limited mobility through the drier area to the South of the mountain range.

The first draft genome of feather grasses using SMRT sequencing and its implications in molecular studies of Stipa

The Eurasian plant Stipa capillata is the most widespread species within feather grasses. Many taxa of the genus are dominants in steppe plant communities and can be used for their classification and in studies related to climate change. Moreover, some species are of economic importance mainly as fodder plants and can be used for soil remediation processes. Although large-scale molecular data has begun to appear, there is still no complete or draft genome for any Stipa species. Thus, here we present a single-molecule long-read sequencing dataset generated using the Pacific Biosciences Sequel System. A draft genome of about 1004 Mb was obtained with a contig N50 length of 351 kb. Importantly, here we report 81,224 annotated protein-coding genes, present 77,614 perfect and 58 unique imperfect SSRs, reveal the putative allopolyploid nature of S. capillata, investigate the evolutionary history of the genus, demonstrate structural heteroplasmy of the chloroplast genome and announce for the first time the mitochondrial genome in Stipa. The assembled nuclear, mitochondrial and chloroplast genomes provide a significant source of genetic data for further works on phylogeny, hybridisation and population studies within Stipa and the grass family Poaceae.

A 313 plastome phylogenomic analysis of Pooideae: Exploring relationships among the largest subfamily of grasses

In this study, we analyzed 313 plastid genomes (plastomes) of Poaceae with a focus on expanding our current knowledge of relationships among the subfamily Pooideae, which represented over half the dataset (164 representatives). In total, 47 plastomes were sequenced and assembled for this study. This is the largest study of its kind to include plastome-level data, to not only increase sampling at both the taxonomic and molecular levels with the aim of resolving complex and reticulate relationships, but also to analyze the effects of alignment gaps in large-scale analyses, as well as explore divergences in the subfamily with an expanded set of 14 accepted grass fossils for more accurate calibrations and dating. Incorporating broad systematic assessments of Pooideae taxa conducted by authors within the last five years, we produced a robust phylogenomic reconstruction for the subfamily, which included all but two supergeneric taxa (Calothecinae and Duthieeae). We further explored how including alignment gaps in plastome analyses oftentimes can produce incorrect or misinterpretations of complex or reticulate relationships among taxa of Pooideae. This presented itself as consistently changing relationships at specific nodes for different stripping thresholds (percentage-based removal of gaps per alignment column). Our summary recommendation for large-scale genomic plastome datasets is to strip alignment columns of all gaps to increase pairwise identity and reduce errant signal from poly A/T bias. To do this we used the "mask alignment" tool in Geneious software. Finally, we determined an overall divergence age for Pooideae of roughly 84.8 Mya, which is in line with, but slightly older than most recent estimates.

Molecular Phylogenetics and Micromorphology of Australasian Stipeae (Poaceae, Subfamily Pooideae), and the Interrelation of Whole-Genome Duplication and Evolutionary Radiations in This Grass Tribe

The mainly Australian grass genus Austrostipa (tribe Stipeae) comprising approximately 64 species represents a remarkable example of an evolutionary radiation. To investigate aspects of diversification, macro- and micromorphological variation in this genus, we conducted molecular phylogenetic and scanning electron microscopy (SEM) analyses including representatives from most of Austrostipa's currently accepted subgenera. Because of its taxonomic significance in Stipeae, we studied the lemma epidermal pattern (LEP) in 34 representatives of Austrostipa. Plastid DNA variation within Austrostipa was low and only few lineages were resolved. Nuclear ITS and Acc1 yielded comparable groupings of taxa and resolved subgenera Arbuscula, Petaurista, and Bambusina in a common clade and as monophyletic. In most of the Austrostipa species studied, the LEP was relatively uniform (typical maize-like), but six species had a modified cellular structure. The species representing subgenera Lobatae, Petaurista, Bambusina as well as A. muelleri from subg. Tuberculatae were well-separated from all the other species included in the analysis. We suggest recognizing nine subgenera in Austrostipa (with number of species): Arbuscula (4), Aulax (2), Austrostipa (36), Bambusina (2), Falcatae (10), Lobatae (5), Longiaristatae (2), Petaurista (2) and the new subgenus Paucispiculatae (1) encompassing A. muelleri. Two paralogous sequence copies of Acc1, forming two distinct clades, were found in polyploid Austrostipa and Anemanthele. We found analogous patterns for our samples of Stipa s.str. with their Acc1 clades strongly separated from those of Austrostipa and Anemanthele. This underlines a previous hypothesis of Tzvelev (1977) that most extant Stipeae are of hybrid origin. We also prepared an up-to-date survey and reviewed the chromosome number variation for our molecularly studied taxa and the whole tribe Stipeae. The chromosome base number patterns as well as dysploidy and whole-genome duplication events were interpreted in a phylogenetic framework. The rather coherent picture of chromosome number variation underlines the enormous phylogenetic and evolutionary significance of this frequently ignored character.

Checklist of the grasses of India

A checklist of the grasses of India is presented, as compiled from survey of all available literature. Of the twelve subfamilies of grasses, ten are represented in India. Most subfamilies have been examined by taxonomic experts for up-to-date nomenclature. The list includes 1506 species plus infraspecific taxa and presents information on types, synonyms, distribution within India, and habit. Twelve new combinations are made, viz. Arctopoa tibetica (Munro ex Stapf) Prob. var. aristulata (Stapf) E.A. Kellogg, comb. nov.; Chimonocalamus nagalandianus (H.B. Naithani) L.G. Clark, comb. nov.; Chionachne digitata (L.f.) E.A. Kellogg, comb. nov.; Chionachne wallichiana (Nees) E.A. Kellogg, comb. nov.; Dinebra polystachyos (R. Br.) E.A. Kellogg, comb. nov.; Moorochloa eruciformis (Sm.) Veldkamp var. divaricata (Basappa & Muniv.) E.A. Kellogg, comb. nov.; Phyllostachys nigra (Lodd. ex Lindl.) Munro var. puberula (Miq.) Kailash, comb. & stat. nov.; Tzveleviochloa schmidii (Hook. f.) E.A. Kellogg, comb. nov.; Urochloa lata (Schumach.) C.E. Hubb. var. pubescens (C.E. Hubb.) E.A. Kellogg, comb. nov.; Urochloa ramosa (L.) T.Q. Nguyen var. pubescens (Basappa & Muniy.) E.A. Kellogg, comb. nov.; Urochloa semiundulata (Hochst. ex A. Rich.) Ashalatha & V.J. Nair var. intermedia (Basappa & Muniy.) E.A. Kellogg, comb. nov.

Eriocoma valdesii, a new species from México (Poaceae, Stipeae)

Eriocoma valdesii sp. nov., is described and illustrated. The new species was found growing on calcareous rocky slopes and hillsides between 1700-2721 m in Coahuila, Nuevo León, San Luis Potosí, and Tamaulipas. The new species is morphologically similar to Eriocoma lobata but differs in having ligules (2-) 4.5-8.5 mm long with acute to narrowly acute and lacerate apices and florets with a sharp-pointed callus. In addition, we include a key to the species of Eriocoma in northeastern México.

A key to the North American genera of Stipeae (Poaceae, Pooideae) with descriptions and taxonomic names for species of Eriocoma, Neotrinia, Oloptum, and five new genera: Barkworthia, ×Eriosella, Pseudoeriocoma, Ptilagrostiella, and Thorneochloa

Based on earlier molecular DNA studies we recognize 14 native Stipeae genera and one intergeneric hybrid in North America. We provide descriptions, new combinations, and 10 illustrations for species of Barkworthia gen. nov., Eriocoma, Neotrinia, Oloptum, Pseudoeriocoma gen. nov., Ptilagrostiella gen. nov., Thorneochloa gen. nov., and ×Eriosella nothogen. nov. The following 40 new combinations are made: Barkworthiastillmanii, Eriocomaalta, E.arida, E.arnowiae, E.bloomeri, E.bracteata, E.contracta, E.coronata, E.curvifolia, E.hendersonii, E.latiglumis, E.lemmonii, E.lemmoniissp.pubescens, E.lettermanii, E.lobata, E.nelsonii, E.nelsoniissp.dorei, E.nevadensis, E.occidentalis, E.occidentalisssp.californica, E.occidentalisssp.pubescens, E.parishii, E.parishiissp.depaupertata, E.perplexa, E.pinetorum, E.richardsonii, E.robusta, E.scribneri, E.swallenii, E.thurberiana, E.wallowaensis, ×Eriosellacaduca, Pseudoeriocomaacuta, P.constricta, P.editorum, P.eminens, P.hirticulmis, P.multinodis, Ptilagrostiellakingii, and Thorneochloadiegoensis. A key to the native and introduced genera of North American Stipeae, and an overview of the tribe in North America and worldwide are given. Lectotypes are designated for Eriocomacuspidata Nutt., Fendleriarhynchelytroides Steud., Stipabloomeri Bol., Stipacoronata Thurb., Stipamembranacea Pursh, Stipamormonum Mez, Stiparichardsonii Link, and Stipawilliamsii Scribn. Achnatherum s.s. and Piptatherum s.s. are now restricted to Eurasia and the Mediterranean/Asia, respectively.

Divergence Estimation in the Presence of Incomplete Lineage Sorting and Migration

This article focuses on the problem of estimating a species tree from multilocus data in the presence of incomplete lineage sorting and migration. I develop a mathematical model similar to IMa2 (Hey 2010) for the relevant evolutionary processes which allows both the population size parameters and the migration rates between pairs of species tree branches to be integrated out. I then describe a BEAST2 package DENIM (Divergence estimation notwithstanding ILS and migration) which is based on this model and which uses an approximation to sample from the posterior. The approximation is based on the assumption that migrations are rare, and it only samples from certain regions of the posterior which seem likely given this assumption. The method breaks down if there is a lot of migration. Using simulations, Leaché et al. (2014) showed that using the standard multispecies coalescent model to infer a species tree can result in poor accuracy if migration is present. I reanalyze this simulated data to explore DENIM's performance and demonstrate substantial improvements in accuracy over *BEAST. I also reanalyze an empirical data set.

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

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 28.7 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 99.9% of grass diversity.

Global grass (Poaceae) success underpinned by traits facilitating colonization, persistence and habitat transformation

Poaceae (the grasses) is arguably the most successful plant family, in terms of its global occurrence in (almost) all ecosystems with angiosperms, its ecological dominance in many ecosystems, and high species richness. We suggest that the success of grasses is best understood in context of their capacity to colonize, persist, and transform environments (the "Viking syndrome"). This results from combining effective long-distance dispersal, efficacious establishment biology, ecological flexibility, resilience to disturbance and the capacity to modify environments by changing the nature of fire and mammalian herbivory. We identify a diverse set of functional traits linked to dispersal, establishment and competitive abilities. Enhanced long-distance dispersal is determined by anemochory, epizoochory and endozoochory and is facilitated via the spikelet (and especially the awned lemma) which functions as the dispersal unit. Establishment success could be a consequence of the precocious embryo and large starch reserves, which may underpin the extremely short generation times in grasses. Post-establishment genetic bottlenecks may be mitigated by wind pollination and the widespread occurrence of polyploidy, in combination with gametic self-incompatibility. The ecological competitiveness of grasses is corroborated by their dominance across the range of environmental extremes tolerated by angiosperms, facilitated by both C₃ and C₄ photosynthesis, well-developed frost tolerance in several clades, and a sympodial growth form that enabled the evolution of both annual and long-lived life forms. Finally, absence of investment in wood (except in bamboos), and the presence of persistent buds at or below ground level, provides tolerance of repeated defoliation (whether by fire, frost, drought or herbivores). Biotic modification of environments via feedbacks with herbivory or fire reinforce grass dominance leading to open ecosystems. Grasses can be both palatable and productive, fostering high biomass and diversity of mammalian herbivores. Many grasses have a suite of architectural and functional traits that facilitate frequent fire, including a tufted growth form, and tannin-like substances in leaves which slow decomposition. We mapped these traits over the phylogeny of the Poales, spanning the grasses and their relatives, and demonstrated the accumulation of traits since monocots originated in the mid-Cretaceous. Although the sympodial growth form is a monocot trait, tillering resulting in the tufted growth form most likely evolved within the grasses. Similarly, although an ovary apparently constructed of a single carpel evolved in the most recent grass ancestor, spikelets and the awned lemma dispersal units evolved within the grasses. Frost tolerance and C₄ photosynthesis evolved relatively late (late Palaeogene), and the last significant trait to evolve was probably the production of tannins, associated with pyrophytic savannas. This fits palaeobotanical data, suggesting several phases in the grass success story: from a late Cretaceous origin, to occasional tropical grassland patches in the later Palaeogene, to extensive C₃ grassy woodlands in the early-middle Miocene, to the dramatic expansion of the tropical C₄ grass savannas and grasslands in the Pliocene, and the C₃ steppe grasslands during the Pleistocene glacial periods. Modern grasslands depend heavily on strongly seasonal climates, making them sensitive to climate change.

Ptilagrostis contracta (Stipeae, Poaceae), a New Species Endemic to Qinghai-Tibet Plateau

A new species, Ptilagrostis contracta, endemic to Qinghai-Tibet Plateau is described and illustrated. It is distinguished from other species in Ptilagrostis by having contracted panicles, 1-geniculate awns with hairy columns and scabrous bristles and evenly pubescent lemmas. Evidence from lemma epidermal pattern, cytology and molecular phylogenetic analyses based on the nuclear ITS sequence data confirm its systematic position in Ptilagrostis.

Species delimitation in plants using the Qinghai-Tibet Plateau endemic Orinus (Poaceae: Tridentinae) as an example

BACKGROUND AND AIMS

Accurate identification of species is essential for the majority of biological studies. However, defining species objectively and consistently remains a challenge, especially for plants distributed in remote regions where there is often a lack of sufficient previous specimens. In this study, multiple approaches and lines of evidence were used to determine species boundaries for plants occurring in the Qinghai-Tibet Plateau, using the genus Orinus (Poaceae) as a model system for an integrative approach to delimiting species.

METHODS

A total of 786 individuals from 102 populations of six previously recognized species were collected for niche, morphological and genetic analyses. Three plastid DNA regions (matK, rbcL and trnH-psbA) and one nuclear DNA region [internal transcribed space (ITS)] were sequenced.

KEY RESULTS

Whereas six species had been previously recognized, statistical analyses based on character variation, molecular data and niche differentiation identified only two well-delimited clusters, together with a third possibly originating from relatively recent hybridization between, or historical introgression from, the other two.

CONCLUSIONS

Based on a principle of integrative species delimitation to reconcile different sources of data, the results provide compelling evidence that the six previously recognized species of the genus Orinus that were examined should be reduced to two, with new circumscriptions, and a third, identified in this study, should be described as a new species. This empirical study highlights the value of applying genetic differentiation, morphometric statistics and ecological niche modelling in an integrative approach to re-circumscribing species boundaries. The results produce relatively objective, operational and unbiased taxonomic classifications of plants occurring in remote regions.

Plastid phylogenomics of the cool-season grass subfamily: clarification of relationships among early-diverging tribes

Whole plastid genomes are being sequenced rapidly from across the green plant tree of life, and phylogenetic analyses of these are increasing resolution and support for relationships that have varied among or been unresolved in earlier single- and multi-gene studies. Pooideae, the cool-season grass lineage, is the largest of the 12 grass subfamilies and includes important temperate cereals, turf grasses and forage species. Although numerous studies of the phylogeny of the subfamily have been undertaken, relationships among some 'early-diverging' tribes conflict among studies, and some relationships among subtribes of Poeae have not yet been resolved. To address these issues, we newly sequenced 25 whole plastomes, which showed rearrangements typical of Poaceae. These plastomes represent 9 tribes and 11 subtribes of Pooideae, and were analysed with 20 existing plastomes for the subfamily. Maximum likelihood (ML), maximum parsimony (MP) and Bayesian inference (BI) robustly resolve most deep relationships in the subfamily. Complete plastome data provide increased nodal support compared with protein-coding data alone at nodes that are not maximally supported. Following the divergence of Brachyelytrum, Phaenospermateae, Brylkinieae-Meliceae and Ampelodesmeae-Stipeae are the successive sister groups of the rest of the subfamily. Ampelodesmeae are nested within Stipeae in the plastome trees, consistent with its hybrid origin between a phaenospermatoid and a stipoid grass (the maternal parent). The core Pooideae are strongly supported and include Brachypodieae, a Bromeae-Triticeae clade and Poeae. Within Poeae, a novel sister group relationship between Phalaridinae and Torreyochloinae is found, and the relative branching order of this clade and Aveninae, with respect to an Agrostidinae-Brizinae clade, are discordant between MP and ML/BI trees. Maximum likelihood and Bayesian analyses strongly support Airinae and Holcinae as the successive sister groups of a Dactylidinae-Loliinae clade.

Untangling reticulate evolutionary relationships among New World and Hawaiian mints (Stachydeae, Lamiaceae)

The phenomenon of polyploidy and hybridization usually results in novel genetic combinations, leading to complex, reticulate evolution and incongruence among gene trees, which in turn may show different phylogenetic histories than the inherent species tree. The largest tribe within the subfamily Lamioideae (Lamiaceae), Stachydeae, which includes the globally distributed Stachys, and one of the largest Hawaiian angiosperm radiations, the endemic mints, is a widespread and taxonomically challenging lineage displaying a wide spectrum of morphological and chromosomal diversity. Previous molecular phylogenetic studies have showed that while the Hawaiian mints group with Mexican-South American Stachys based on chloroplast DNA sequence data, nuclear ribosomal DNA (nrDNA) sequences suggest that they are most closely related to temperate North American Stachys. Here, we have utilized five independently inherited, low-copy nuclear loci, and a variety of phylogenetic methods, including multi-locus coalescence-based tree reconstructions, to provide insight into the complex origins and evolutionary relationships between the New World Stachys and the Hawaiian mints. Our results demonstrate incongruence between individual gene trees, grouping the Hawaiian mints with both temperate North American and Meso-South American Stachys clades. However, our multi-locus coalescence tree is concurrent with previous nrDNA results placing them within the temperate North American Stachys clade. Our results point toward a possible allopolyploid hybrid origin of the Hawaiian mints arising from temperate North American and Meso-South American ancestors, as well as a reticulate origin for South American Stachys. As such, our study is another significant step toward further understanding the putative parentage and the potential influence of hybridization and incomplete lineage sorting in giving rise to this insular plant lineage, which following colonization underwent rapid morphological and ecological diversification.

Historical biogeography of Haloragaceae: an out-of-Australia hypothesis with multiple intercontinental dispersals

Haloragaceae are a cosmopolitan plant family with its centre of diversity in Australia. Here, we investigate the historical biogeography of the family and the role of vicariance or dispersal in shaping its current distribution. DNA sequences from ITS, matK and the trnK 5' and trnK 3' introns were obtained for 102 species representing all 8 genera of Haloragaceae for use in Bayesian molecular dating. Molecular dating was conducted using two macrofossils as calibration points for the analyses. Biogeographic history was investigated using a Bayesian dispersal-vicariance analysis and a dispersal-extinction-cladogenesis model. The results suggest that the earliest diversification of the extant Haloragaceae occurred in Australia during the Eocene (37.3-56.3Ma). Early diversification of the family in the Southern Hemisphere is inferred as resulting from vicariance events among Australia, South America and New Zealand. The results also indicate multiple out of Australia dispersal routes, primarily including (1) from Australia to Asia during the Miocene, with subsequent dispersal to Europe and North America; (2) from Australia to New Zealand, then to South America during the Miocene and Pliocene. Most of the inferred dispersal events occurred throughout the Miocene and later, and are biased towards the aquatic Haloragaceae lineages.