No full-text available
To read the full-text of this research,
you can request a copy directly from the authors.
Phylogeny, biogeography, reticulation, and classification of Agrostis (Poaceae: Pooideae: Poeae: Agrostidinae) with expansion of Polypogon to include Lachnagrostis (in part)
Abstract
To investigate the evolutionary relationships and biogeographical history among the species of Agrostis and allied genera within the subtribe Agrostidinae, we generated a phylogeny based on sequences from nuclear ribosomal DNA (ITS) and three plastid regions ( rpl32‐trnL spacer, rps16‐trnK spacer, and rps16 intron). We also aimed to assess the generic limits of Agrostis , characterize possible subgeneric relationships among species in the genus, identify hypothesized reticulation events, and present our biogeographical theory. Based on our phylogeny of 198 samples, representing 138 species (82 from Agrostis as currently recognized, 10 from Polypogon , and 10 from Lachnagrostis ), we identify two strongly supported clades within Agrostis : clade Longipaleata ( Agrostis subg. Vilfa ) and clade Brevipaleata ( A . subg. Agrostis ). The species of Agrostis in clade Longipaleata usually have florets with paleas 2/5 to as long as the lemma, whereas species in clade Brevipaleata have florets with paleas less than 2/5 as long as the lemma, minute, or absent. Core (species with congruent alignment using ITS and plastid data) phylogenetic analysis of Agrostis reveals three strongly supported clades within Longipaleata (European‐Northwest African, Asian, and African), three strongly supported clades within Brevipaleata (Asian, North American, and South American), and a European grade leading to the latter two. Of the six genera commonly associated with Agrostis , that is, Bromidium , Polypogon, Lachnagrostis, Linkagrostis, Chaetopogon, and Chaetotropis , only Polypogon maintained its status as a separate genus, while the remaining genera are subsumed within Agrostis or Polypogon . Polypogon is identified as an intergeneric hybrid originating via ancient hybridization between unknown representatives of Agrostis clade Longipaleata (plastid DNA) and Calamagrostis clade Americana (nrDNA). We include several species of Lachnagrostis , including the type ( L. filiformis ), that follow the same pattern in Polypogon , while the remaining species of Lachnagrostis in our study are identified as ancient intersubgeneric hybrids within Agrostis . We propose nine new combinations in Polypogon : P. adamsonii (Vickery) P.M. Peterson, Soreng & Romasch.; P. aemulus (R. Br.) P.M. Peterson, Soreng & Romasch.; P. billardierei (R. Br.) P.M. Peterson, Soreng & Romasch.; P. bourgaei (E. Fourn.) P.M. Peterson, Soreng & Romasch.; P. filiformis (G. Forst.) P.M. Peterson, Soreng & Romasch.; P. littoralis P.M. Peterson, Soreng & Romasch.; P. exaratus (Trin.) P.M. Peterson, Soreng & Romasch.; P. polypogonoides (Stapf) P.M. Peterson, Soreng & Romasch.; and P. reuteri (Boiss.) P.M. Peterson, Soreng & Romasch. We designate lectotypes for the names Agrostis sect. Aristatae Willd., Agrostis barbuligera Stapf, A. bourgaei E. Fourn., A. eriantha Hack., A. exarata Trin., A. lachnantha Nees, A. polypogonoides Stapf, Chaetotropis chilensis Kunth, Polypogon elongatus Kunth, P. inaequalis Trin., P. suspicatus Willd., and Vilfa muricata J. Presl .
ResearchGate has not been able to resolve any citations for this publication.
Koelerioid grasses (subtribe Aveninae, tribe Poeae; Pooideae) resolve into two major clades, here called Koelerioid Clades A and B. Phylogenetic relationships among koelerioid grasses are investigated using plastid DNA sequences of rpl32-trnL, rps16-trnK, rps16 intron, and ITS regions, focusing on Trisetum, Acrospelion, and some annual species (Rostraria p.p. and Trisetaria p.p.) closely related to Trisetum flavescens in Koelerioid Clade A. Phylogenetic analyses of several selected data sets performed for 80 taxa and using maximum likelihood and Bayesian methods, revealed mostly congruent topologies in the nuclear and plastid trees, but also reticulation affecting several lineages. Trisetum is restricted to one species, T. flavescens, which is a sister to the clade formed by Trisetum gracile and Trisetaria aurea. The latter two species are classified here in the genus Graciliotrisetum gen. nov. The sister clade includes three species of Rostraria and Trisetaria lapalmae, all of which are classified here in a resurrected genus, Aegialina, which includes four species. Acrospelion is enlarged to include 13 species after the addition of other species formerly classified in Trisetum sect. Trisetum and T. sect. Acrospelion. We also transfer Trisetum ambiguum, Trisetum longiglume, and Koeleria mendocinensis to Graphephorum; and Helictotrichon delavayi to Tzveleviochloa, expanding these genera to eight and six species, respectively. We evaluate cases of reticulate evolution between Koelerioid Clades A and B and within Koelerioid Clade A, which probably gave rise to Graphephorum, Rostraria cristata, and Rostraria obtusiflora. Finally, we comment on polyploidy and biogeographic patterns in koelerioid grasses. We propose 26 new combinations. Lectotypes are designated for 14 names and a neotype for Alopecurus litoreus.
Röser, M. & Tkach, N. 2024: Delimitation and nomenclature of Agrostis, Polypogon and related grasses (Poaceae subfamily Pooideae). Schlechtendalia 41: 6367. Recent descriptions of new genera and revised genus delimitations have resulted in numerous changes in the taxonomy of the grass subtribe Agrostidinae. Among the remaining unresolved questions is the distinction between the genera Agrostis and Polypogon. Molecular phylogenetic data suggest that Polypogon is embedded in Agrostis and both genera should be unified. To implement the necessary nomenclatural changes, several new combinations are made and some new names are introduced.
Agrostis is one of the most diverse genera of the Poaceae, including ca. 198 species, principally distributed in cold and temperate regions of the world, but also found in the high mountains of the tropics. We present a revision based on morphoanatomical evidence, for the biogeographic region known as Megamexico 3 (i.e., Mexico including the desert areas of southern USA and the Central America territory, to northern Nicaragua). We include taxonomic descriptions and an identification key for the found taxa, maps with the known geographical distribution of the species, and figures with the morphoanatomical characteristics, elevation and phenology. Agrostis is represented in the study zone by 20 species, of which four are endemic and three are introduced. Most records of the genus are distributed in the mountains, above 1500 m a.s.l., in open areas of temperate forests, with conifers and Quercus . Specimens with spikelets occur year round, but most records occur during the wet season, in the months of July to October. We propose a preliminary conservation assessment for each species in the study zone, according to the International Union for Conservation of Nature categories: one with Deficient Data (DD), six as Endangered (EN), two as Vulnerable (VU), and 11 as Least Concern (LC).
We describe a new grass species, Agrostis swalalahos, endemic to several peaks in the northwestern Coast Range of Clatsop County, Oregon, U.S.A.
The classical model of concerted evolution states that hundreds to thousands of ribosomal DNA (rDNA) units undergo homogenization, making the multiple copies of the individual units more uniform across the genome than would be expected given mutation frequencies and gene redundancy. While the universality of this over 50-year-old model has been confirmed in a range of organisms, advanced high throughput sequencing techniques have also revealed that rDNA homogenization in many organisms is partial and, in rare cases, even apparently failing. The potential underpinning processes leading to unexpected intragenomic variation have been discussed in a number of studies, but a comprehensive understanding remains to be determined. In this work, we summarize information on variation or polymorphisms in rDNAs across a wide range of taxa amongst animals, fungi, plants, and protists. We discuss the definition and description of concerted evolution and describe whether incomplete concerted evolution of rDNAs predominantly affects coding or non-coding regions of rDNA units and if it leads to the formation of pseudogenes or not. We also discuss the factors contributing to rDNA variation, such as interspecific hybridization, meiotic cycles, rDNA expression status, genome size, and the activity of effector genes involved in genetic recombination, epigenetic modifications, and DNA editing. Finally, we argue that a combination of approaches is needed to target genetic and epigenetic phenomena influencing incomplete concerted evolution, to give a comprehensive understanding of the evolution and functional consequences of intragenomic variation in rDNA.
Grasses are widespread on every continent and are found in all terrestrial biomes. The dominance and spread of grasses and grassland ecosystems have led to significant changes in Earth’s climate, geochemistry, and biodiversity. The abundance of DNA sequence data, particularly chloroplast sequences, and advances in placing grass fossils within the family allows for a reappraisal of the family's origins, timing, and geographic spread and the factors that have promoted diversification. We reconstructed a time-calibrated grass phylogeny and inferred ancestral areas using chloroplast DNA sequences from nearly 90% of extant grass genera. With a few notable exceptions, the phylogeny is well resolved to the subtribal level. The family began to diversify in the Early–Late Cretaceous (crown age of 98.54 Ma) on West Gondwana before the complete split between Africa and South America. Vicariance from the splitting of Gondwana may be responsible for the initial divergence in the family. However, Africa clearly served as the center of origin for much of the early diversification of the family. With this phylogenetic, temporal, and spatial framework, we review the evolution and biogeography of the family with the aim to facilitate the testing of biogeographical hypotheses about its origins, evolutionary tempo, and diversification. The current classification of the family is discussed with an extensive review of the extant diversity and distribution of species, molecular and morphological evidence supporting the current classification scheme, and the evidence informing our understanding of the biogeographical history of the family.
We present an updated worldwide phylogenetic classification of Poaceae with 11,783 species in 12 subfamilies, seven supertribes, 54 tribes, five supersubtribes, 109 subtribes, and 789 accepted genera. The subfamilies (in descending order based on the number of species) are Pooideae with 4126 species in 219 genera, 15 tribes, and 34 subtribes; Panicoideae with 3325 species in 242 genera, 14 tribes, and 24 subtribes; Bambusoideae with 1698 species in 136 genera, three tribes, and 19 subtribes; Chloridoideae with 1603 species in 121 genera, five tribes, and 30 subtribes; Aristidoideae with 367 species in three genera, and one tribe; Danthonioideae with 292 species in 19 genera, and one tribe; Micrairoideae with 192 species in nine genera, and three tribes; Oryzoideae with 117 species in 19 genera, four tribes, and two subtribes; Arundinoideae with 36 species in 14 genera, three tribes; 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. Two new tribes and 22 new or resurrected subtribes are recognized. Forty‐five new (28) and resurrected (17) genera are accepted, and 24 previously accepted genera are placed in synonymy. We also provide an updated list of all accepted genera including common synonyms, genus authors, number of species in each accepted genus, and subfamily affiliation. The following seven new combinations are made in Lorenzochloa: L. bomanii, L. henrardiana, L. mucronata, L. obtusa, L. orurensis, L. rigidiseta, and L. venusta. This article is protected by copyright. All rights reserved.
To investigate the evolutionary relationships and biogeographical history among the species of Calamagrostis and other members of subtribe Agrostidinae, Calothecinae, Echinopogoninae, and Paramochloinae, we generated a phylogeny based on DNA sequences from one nuclear ribosomal and three plastid areas (ITS, rpl32‐trnL spacer, rps16‐trnK spacer, and rps16 intron). Based on our phylogeny, we identify seven species groups (clades) within Calamagrostis: the Meridionalis group comprises two species from Central and South America, the Americana group comprises species from North America, the Deyeuxia and Epigeios groups comprises species from Eurasia, the Orientalis group comprises species from East Asia, the Purpurea group comprises species from Eurasia and North America, and the Calamagrostis group comprises species from Eurasia and North America. We hypothesize that Calamagrostis originated in North America with the primary split of the Meridionalis group, followed by split between autochthonous Americana group and two future Eurasian branches encompassing all remaining groups, which possibly dispersed in Eurasia independently. The molecular data suggest that hybridization and genomic introgression played a prominent role in the evolutionary history of Calamagrostis. We propose a new genus, Condilorachia, segregated from Trisetum s.l., with three species from South America for which we propose new combinations: Condilorachia bulbosa, C. brasiliensis, and C. juergensii; a new combination in Greeneochloa, G. expansa; and the subsumption of Dichelachne into Pentapogon with 20 new combinations: Pentapogon avenoides, P. brassii, P. chaseianus, P. crinita, P. densus, P. frigidus, P. gunnianus, P. hirtella, P. inaequiglumis, P. lautumia, P. micrantha, P. parva, P. quadrisetus, P. rara, P. robusta, P. scaberulus, P. sclerophyllus, P. suizanensis, P. sieberiana, and P. validus. We provide a diagnosis, description, and a key to the species of Condilorachia. This article is protected by copyright. All rights reserved.
The circumscription of the grass subtribe Calothecinae has undergone several changes since its description. Currently, it comprises Chascolytrum and the recently described genera Laegaardia and Paramochloa. Here we evaluate the circumscription of Calothecinae and the recently proposed infrageneric classification of Chascolytrum based on a phylogeny with more comprehensive taxon and molecular marker sampling than in previous studies. We sampled all Calothecinae genera, all but one Chascolytrum species, two South American Trisetum s.l. and representatives of the subtribes Agrostidinae, Brizinae, Echinopogoninae, Koeleriinae, Phalaridinae, and Torreyochloinae within Poaceae tribe Poeae. We performed Bayesian and Maximum Likelihood analyses of four plastid DNA regions (atpF‐atpH, matK, rps16 intron, and trnL‐trnF) and two nuclear ribosomal regions (ITS and ETS). Our results revealed that neither Calothecinae nor Chascolytrum is monophyletic as currently recognized because Trisetum brasiliense and T. bulbosum are nested within Chascolytrum. We include these two Trisetum species in Calothecinae as incertae sedis. Laegaardia and Paramochloa form a clade that is sister to the Chascolytrum + Trisetum clade, and based on morphological characters we transfer the former to the new subtribe Paramochloinae. Our Chascolytrum phylogeny is better resolved and supported than in previous studies, and based on these results we divide Chascolytrum into nine genera, including two new ones: Boldrinia (gen. nov.), Calotheca, Chascolytrum, Erianthecium, Lombardochloa, Microbriza, Poidium, Rhombolytrum, and Rosengurttia (gen. nov.). We provide a key to Calothecinae genera, descriptions of the genera, nomenclatural information, and keys to species of each genus. In addition, six new combinations are proposed.
This article is protected by copyright. All rights reserved.
Based on a molecular DNA phylogeny of three plastid (rpl32-trnK, rps16 intron, and rps16-trnK) and nuclear ITS regions investigating 32 species of Agrostidinae, we describe two new genera, Agrostula gen. nov. with a single species and Alpagrostis gen. nov. with four species; provide support for five species in a monophyletic Podagrostis; and include a small sample of 12 species of a monophyletic Agrostis s.s. (including the type and most species of Neoschischkinia), that separates into two clades corresponding to A. subg. Agrostis and A. subg. Vilfa. Agrostula differs from Agrostis in having leaf blades with pillars of sclerenchyma which are continuous between the adaxial and abaxial surface of the blades, dorsally rounded glumes with blunt to truncate and erose to denticulate apices, florets ½ the length of the glumes, lemmas equally wide as long, widest at (or near) apex, apices broadly truncate, irregularly 5 to 7 denticulate to erose, awnless, anthers longer than the lemmas, and rugose-papillose caryopses. Alpagrostis differs from Agrostis in having geniculate basally inserted awns and truncate lemma apices with lateral veins prolonged from the apex in (2)4 setae. The following eight new combinations are made: Agrostula truncatula, Agrostula truncatula subsp. durieui, Alpagrostis alpina, Alpagrostis alpina var. flavescens, Alpagrostis barceloi, Alpagrostis setacea, Alpagrostis setacea var. flava, and Alpagrostis schleicheri. In addition, we provide a key separating Agrostula and Alpagrostis from Agrostis s.s. and other genera previously considered as synonyms of Agrostis; lectotypify Agrostis alpina Scop., A. schleicheri Jord. & Verl., A. truncatula Parl., and A. truncatula var. durieui Henriq.; and neotypify A. setacea Curtis.
Based on morphological study and corroborated by unpublished molecular phylogenetic analyses, five grass species of high-mountain grasslands in Mexico, Central and South America, Agrostis bacillata , A. exserta , A. liebmannii , A. rosei , and A. trichodes , are transferred to Podagrostis and bring the number of species of this genus recognized in the New World to ten. The name Apera liebmannii is lectotypified and epitypified. We provide an updated genus description for Podagrostis , and updated species descriptions, images, and notes on the new combinations. The diagnostic characteristics differentiating Podagrostis from Agrostis are: a) palea that reaches from (2/3) ¾ to almost the apex of the lemma; b) florets that usually almost equal the length of the glumes or are at least ¾ the length of the glumes; c) rachilla extension present and emerging from under the base of the palea as a slender short stub (rudimentary or up to 1.4 mm long, sometimes obscure in most florets in P. rosei ), smooth or scaberulous, glabrous or distally pilulose (hairs < 0.3 mm long); d) lemmas usually awnless, sometimes with a short straight awn 0.2–0.6 mm long, inserted medially or in the upper 1/3 of the lemma, not surpassing the glumes (awn well-developed, straight or geniculate and inserted in lower 1/3 of lemma, not or briefly surpassing glumes in P. rosei ). We include a generic key to distinguish the species of Podagrostis from other similar genera in Latin America and a key to distinguish the species of Podagrostis now accepted as occurring in these areas.
To investigate the evolutionary diversification and morphological evolution of grass supertribe Poodae (subfam. Pooideae, Poaceae) we conducted a comprehensive molecular phylogenetic analysis including representatives from most of its accepted genera. We focused on generating a DNA sequence dataset of plastid matK gene–3′trnK exon and trnL-trnF regions and nuclear ribosomal (nr) ITS1–5.8S gene–ITS2 and ETS that was taxonomically overlapping as completely as possible (altogether 257 species). The idea was to infer whether phylogenetic trees or certain clades based on plastid and nrDNA data correspond with each other or discord, revealing signatures of past hybridization. The datasets were analysed separately, in combination, by excluding taxa with discordant placements in the individual gene trees and with duplication of these taxa in away that each duplicate has only one data partition (plastid or nrDNA). We used maximum likelihood, maximum parsimony and Bayesian approaches. Instances of severe conflicts between the phylogenetic trees derived from both datasets, some of which have been noted earlier, point to hybrid origin of several lineages such as the ABCV clade encompassing several subtribes and subordinate clades, subtribes Airinae, Anthoxanthinae, Antinoriinae, subtr. nov., Aristaveninae, Avenulinae, subtr. nov., Helictochloinae, subtr. nov., Holcinae, Phalaridinae, Scolochloinae, Sesleriinae, Torreyochloinae and genera Arctopoa, Castellia, Graphephorum, Hyalopodium, Lagurus, Macrobriza, Puccinellia plus Sclerochloa, Sesleria, Tricholemma, Tzveleviochloa, etc. ‘Calamagrostis’ flavens appears to be an intergeneric hybrid between Agrostis and Calamagrostis. Analyses excluding all lineages with demonstrably cytonuclear discordance revealed three supported main clades within Poodae that were present in both the plastid and nrDNA trees. They fully corresponded in their delineation but were phylogenetically differently arranged, pointing to hybrid origin of one of them. We propose to consider these main clades in classification as separate tribes Aveneae, Poeae s.str. and Festuceae with a phylogenetic arrangement of Aveneae(Poeae,Festuceae) in plastid versus Festuceae (Aveneae,Poeae) in nrDNA trees. Phylogenetic incongruence of the plastid and nuclear markers extends across all hierarchical taxonomic levels of Poodae, ranging from species (not studied here) to genera, subtribes and tribes, therefore the deepest taxonomic levels, emphasizing the enormous significance of reticulate evolution in this large group of grasses. A partly revised classification is presented, including the introduction of a new tribe Festuceae and a re-instatement of tribe Aveneae. Following a comparatively narrow delineation of preferably monophyletic subtribes, Antinoriinae, Avenulinae, Brizochloinae, Helictochloinae and Hypseochloinae are described as new. New genera are Arctohyalopoa and Hyalopodium. New combinations are Anthoxanthum glabrum subsp. sibiricum, A. nitens subsp. kolymense, Arctohyalopoa ivanovae, A. jurtzevii, A. lanatiflora, A. momica, Colpodium biebersteinianum, C. kochii, C. pisidicum, C. trichopodum, C. verticillatum, Dupontia fulva, Festuca masafuerana, F. robinsoniana, Graphephorum canescens, G. cernuum, Hyalopodium araraticum, Paracolpodium baltistanicum, Parapholis cylindrica, P. ×pauneroi. Festuca dolichathera and F. masatierrae are new names.
Based on morphological and molecular evidence we transfer the species of Trisetum sect. Trisetaera, T. hispidum, and Trisetokoeleria taymirica into Koeleria, describe Koeleria sect. Hispanica, and provide a new generic emendation. A total of 49 new combinations or new names are included. Additionally, we lectotypify Avena clarkei Hook f., Avena micans Hook. f., Avena subalpestris Hartm., Avena subspicata var. agrostidea Laest., Trisetum pubiflorum Hack., Trisetum spicatum f. minor Kom., and Trisetum spicatum f. umbrosum Kom.
Based on morphological and molecular evidence we present new combinations or new names for 77 taxa of Cinnagrostis, seven taxa of Deschampsia, and 24 taxa of Peyritschia; and describe three new genera, Greeneochloa P.M. Peterson, Soreng, Romasch. & Barberá, gen. nov. (subtribe Echinopogoninae), Paramochloa P.M. Peterson, Soreng, Romasch. & Barberá, gen. nov. (subtribe Calothecinae), and Laegaardia P.M. Peterson, Soreng, Romasch. & Barberá, gen. nov. (subtribe Calothecinae) with two, two and one species, respectively. In addition to the 116 new taxonomic entities, we provide a key to the genera of American grasses presently or formerly treated in Calamagrostis or Deyeuxia and generic emendations for Cinnagrostis and Peyritschia.
Based on morphological and molecular evidence we present new combinations or new names for 77 taxa of Cinnagrostis, seven taxa of Deschampsia, and 24 taxa of Peyritschia; and describe three new genera, Greeneochloa P.M. Peterson, Soreng, Romasch. & Barberá, gen. nov. (subtribe Echinopogoninae), Paramochloa P.M. Peterson, Soreng, Romasch. & Barberá, gen. nov. (subtribe Calothecinae), and Laegaardia P.M. Peterson, Soreng, Romasch. & Barberá, gen. nov. (subtribe Calothecinae) with two, two and one species, respectively. In addition to the 116 new taxonomic entities, we provide a key to the genera of American grasses presently or formerly treated in Calamagrostis or Deyeuxia and generic emendations for Cinnagrostis and Peyritschia.
Chascolytrum, as currently circumscribed, includes 22-23 South American species that were previously included in nine different genera (Chascolytrum, Briza, Poidium, Calotheca, Microbriza, Gymnachne, Rhombolytrum, Lombardochloa and Erianthecium). Due to the remarkable morphological diversity, the relationships in Chascolytrum s.l. have remained poorly understood, and no infrageneric classification could be proposed based on the latest molecular phylogenetic studies. In this study, we combined molecular (GBSSI, trnL-trnL-trnF and rps16 intron) and morphological characters to investigate the phylogenetic relationships in Chascolytrum s.l. Based on this, morphologically diagnosable clades were recognized as eight sections (Calotheca, Chascolytrum, Hildaea, Lombardochloa, Microbriza, Obovatae, Poidium and Tricholemma), of which three are new and three are monospecific. We describe each section and discuss the new infrageneric classification in comparison with the previous infrageneric classification proposed for the group under the genus Briza. A taxonomic key and images for most of the species in each section are provided. Last, the use of single-copy nuclear genes and morphological data for future phylogenetic reconstructions encompassing Chascolytrum is highlighted.
To investigate the evolutionary relationships among the species of Trisetum and other members of subtribe Koeleriinae a phylogeny based on DNA sequences from four gene regions (ITS, rpl32‐trnL spacer, rps16‐trnK spacer, and rps16 intron) is presented. The analyses, including type species of all genera in Koeleriinae (Acrospelion, Avellinia, Cinnagrostis, Gaudinia, Koeleria, Leptophyllochloa, Limnodea, Peyritschia, Rostraria, Sphenopholis, Trisetaria, Trisetopsis, Trisetum), along with three outgroups, confirms previous indications of extensive polyphyly of Trisetum. Here we focus on the monophyletic Trisetum sect. Sibirica clade that we interpret here as a distinct genus, Sibirotrisetum gen. nov. We include a description of Sibirotrisetum with the following seven new combinations: Sibirotrisetum aeneum, S. bifidum, S. henryi, S. scitulum, S. sibiricum, S. sibiricum subsp. litorale, and S. turcicum; and a single new combination in Acrospelion: A. distichophyllum. Trisetum s.s. is limited to 1, 2 or 3 species pending further study. This article is protected by copyright. All rights reserved.
The exchange of biotas between Eurasia and North America across the Bering Land Bridge had a major impact on ecosystems of both continents throughout the Cenozoic. This exchange has received particular attention regarding placental mammals dispersing into the Americas, including humans after the last glacial period, and also as an explanation for the disjunct distribution of related seed plants in eastern Asia and eastern North America. Here we investigated the bi-directional dispersal across the Bering Land Bridge from estimates of dispersal events based on time-calibrated phylogenies of a broad range of plant, fungus, and animal taxa. We revealed a long-lasting phase of asymmetrical biotic interchange, with a peak of dispersal from Asia into North America during the Late Oligocene warming (26–24 Ma), when dispersal in the opposite direction was greatly decreased. Influx from North America into Asia was lower than in the opposite direction throughout the Cenozoic, but with peak rates of dispersal at the end of the Eocene (40–34 Ma) and again in the Early to Middle Miocene (16–14 Ma). The strong association between dispersal patterns and environmental changes suggests that plants, fungi, and animals have likely dispersed from stable to perturbed environments of North America and Eurasia throughout the Cenozoic.
The standard bootstrap (SBS), despite being computationally intensive, is widely used in maximum likelihood phylogenetic analyses. We recently proposed the ultrafast bootstrap approximation (UFBoot) to reduce computing time while achieving more unbiased branch supports than SBS under mild model violations. UFBoot has been steadily adopted as an efficient alternative to SBS and other bootstrap approaches.
Here, we present UFBoot2, which substantially accelerates UFBoot and reduces the risk of overestimating branch supports due to polytomies or severe model violations. Additionally, UFBoot2 provides suitable bootstrap resampling strategies for phylogenomic data. UFBoot2 is 778 times (median) faster than SBS and 8.4 times (median) faster than RAxML rapid bootstrap on tested datasets. UFBoot2 is implemented in the IQ-TREE software package version 1.6 and freely available at http://www.iqtree.org.
Circumscriptions of and relationships among many genera and suprageneric taxa of the diverse grass tribe Poeae remain controversial. In an attempt to clarify these, we conducted phylogenetic analyses of >2400 new DNA sequences from two nuclear ribosomal regions (ITS, including internal transcribed spacers 1 and 2 and the 5.8S gene, and the 3’-end of the external transcribed spacer (ETS)) and five plastid regions (matK, trnL–trnF, atpF–atpH, psbK–psbI, psbA–rps19–trnH), and of more than 1000 new and previously published ITS sequences, focused particularly on Poeae chloroplast group 1 and including broad and increased species sampling compared to previous studies. Deep branches in the combined plastid and combined ITS+ETS trees are generally well resolved, the trees are congruent in most aspects, branch support across the trees is stronger than in trees based on only ITS and fewer plastid regions, and there is evidence of conflict between data partitions in some taxa. In plastid trees, a strongly supported clade corresponds to Poeae chloroplast group 1 and includes Agrostidinae p.p., Anthoxanthinae, Aveninae s.str., Brizinae, Koeleriinae (sometimes included in Aveninae s.l.), Phalaridinae and Torreyochloinae. In the ITS+ETS tree, a supported clade includes these same tribes as well as Sesleriinae and Scolochloinae. Aveninae s.str. and Sesleriinae are sister taxa and form a clade with Koeleriinae in the ITS+ETS tree whereas Aveninae s.str. and Koeleriinae form a clade and Sesleriinae is part of Poeae chloroplast group 2 in the plastid tree. All species of Trisetum are part of Koeleriinae, but the genus is polyphyletic. Koeleriinae is divided into two major subclades: one comprises Avellinia, Gaudinia, Koeleria, Rostraria, Trisetaria and Trisetum subg. Trisetum, and the other Calamagrostis/Deyeuxia p.p. (multiple species from Mexico to South America), Peyritschia, Leptophyllochloa, Sphenopholis, Trisetopsis and Trisetum subg. Deschampsioidea. Graphephorum, Trisetumcernuum, T.irazuense and T.macbridei fall in different clades of Koeleriinae in plastid vs. nuclear ribosomal trees, and are likely of hybrid origin. ITS and matK trees identify a third lineage of Koeleriinae corresponding to Trisetumsubsect.Sibirica, and affinities of Lagurusovatus with respect to Aveninae s.str. and Koeleriinae are incongruent in nuclear ribosomal and plastid trees, supporting recognition of Lagurus in its own subtribe. A large clade comprises taxa of Agrostidinae, Brizinae and Calothecinae, but neither Agrostidinae nor Calothecinae are monophyletic as currently circumscribed and affinities of Brizinae differ in plastid and nuclear ribosomal trees. Within this clade, one newly identified lineage comprises Calamagrostiscoarctata, Dichelachne, Echinopogon (Agrostidinae p.p.) and Relchela (Calothecinae p.p.), and another comprises Chascolytrum (Calothecinae p.p.) and Deyeuxiaeffusa (Agrostidinae p.p.). Within Agrostidinae p.p., the type species of Deyeuxia and Calamagrostis s.str. are closely related, supporting classification of Deyeuxia as a synonym of Calamagrostis s.str. Furthermore, the two species of Ammophila are not sister taxa and are nested among different groups of Calamagrostis s.str., supporting their classification in Calamagrostis. Agrostis, Lachnagrostis and Polypogon form a clade and species of each are variously intermixed in plastid and nuclear ribosomal trees. Additionally, all but one species from South America classified in Deyeuxiasect.Stylagrostis resolve in Holcinae p.p. (Deschampsia). The current phylogenetic results support recognition of the latter species in Deschampsia, and we also demonstrate Scribneria is part of this clade. Moreover, Holcinae is not monophyletic in its current circumscription because Deschampsia does not form a clade with Holcus and Vahlodea, which are sister taxa. The results support recognition of Deschampsia in its own subtribe Aristaveninae. Substantial further changes to the classification of these grasses will be needed to produce generic circumscriptions consistent with phylogenetic evidence. The following 15 new combinations are made: Calamagrostis×calammophila, C.breviligulata, C.breviligulatasubsp.champlainensis, C.×don-hensonii, Deschampsiaaurea, D.bolanderi, D.chrysantha, D.chrysanthavar.phalaroides, D.eminens, D.eminensvar.fulva, D.eminensvar.inclusa, D.hackelii, D.ovata, and D.ovata var. nivalis. D.podophora; the new name Deschampsiaparodiana is proposed; the new subtribe Lagurinae is described; and a second-step lectotype is designated for the name Deyeuxiaphalaroides.
We present a new worldwide phylogenetic classification of 11 506 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.
This identification guide relies primarily on the use of keys and descriptive information to aid the use in identifying a grass species. It contains some of the best information needed to identify southern African grasses. Keys to grass genera and species are provided, and in some instances also keys to easily confused taxa. For each species, a combination of useful characters is provided, and where applicable, line drawings of the spikelet or parts thereof accompany the identification keys. Species descriptions and distribution maps are hugely important and add to the identification of grasses.
Morphologically, the tribe Cynodonteae is a diverse group of grasses containing about 839 species in 96 genera and 18 subtribes, found primarily in Africa, Asia, Australia, and the Americas. Because the classification of these genera and species has been poorly understood, we conducted a phylogenetic analysis on 213 species (389 samples) in the Cynodonteae using sequence data from seven plastid regions ( rps16-trnK spacer, rps16 intron, rpoC2 , rpl32-trnL spacer, ndhF , ndhA intron, ccsA ) and the nuclear ribosomal internal transcribed spacer regions (ITS 1 & 2) to infer evolutionary relationships and refine the current classification. The phylogenetic tree from the combined plastid and nuclear region is well resolved depicting a strongly supported monophyletic Cynodonteae that includes 17 strongly supported clades corresponding to the subtribes Tripogoninae, Pappophorinae, Traginae, Muhlenbergiinae, Hilariinae, Scleropogoninae, Boutelouinae, Monanthochloinae, Dactylocteniinae, Eleusininae, Aeluropodinae, Triodiinae, Orcuttiinae, Zaqiqahinae, Farragininae, Perotidinae, and Gouiniinae, and two moderately supported clades corresponding to the Orininae and Hubbardochloinae. The plastid data places Odyssea paucinervis as sister to Neobouteloua in the Dactylocteniinae whereas the nuclear ITS data places it as sister to Aeluropus in the Aeluropodinae. Odyssea mucronata is strongly supported sister to the Cteniinae, Trichoneurinae, Farragininae, Perotidinae, Hubbardochloinae, and the Gouiniinae, and not closely related to Odyssea paucinervis . The nuclear data placed Acrachne racemosa as sister to Dactyloctenium in the Dactylocteniinae while the plastid data places it near the base of the Eleusininae. Our new classification recognizes three new subtribes (bringing the total to 21 subtribes): Dactylocteniinae that includes Acrachne , Brachychloa , Dactyloctenium , and Neobouteloua ; Orininae with Cleistogenes and Orinus ; and Zaqiqahinae with a single genus, Zaqiqah gen. nov.; Hubbardochloinae (resurrected here) with seven genera; and describes four new genera: Orthacanthus (Traginae) with a single species, Triplasiella (Gouiniinae) with a single species, Tripogonella (Tripogoninae) with three species, and Zaqiqah with a single species. We additionally provide a subgeneric classification of Distichlis recognizing three sections: D . sect. Monanthochloe , D. sect. Bajaenses , and D . sect. Spicatae , the latter two representing new sections. The following nine new combinations are made: Distichlis sect. Monanthochloe , Orthacanthus pedunculatus , Tridentopsis buckleyana , Tridentopsis mutica var. elongata , Triplasiella eragrotoides , Tripogonella loliiformis , Tripogonella minima , Tripogonella spicata , and Zaqiqah mucronata . We lectotypify the following five names: Festuca loliiformis , F. minima , F. mucronata , Triodia eragrostoides , and Uralepis elongata .
Shifts in the latitude of the intertropical convergence zone - a region of intense tropical rainfall - have often been explained through changes in the atmospheric energy budget, specifically through theories that tie rainfall to meridional energy fluxes. These quantitative theories can explain shifts in the zonal mean, but often have limited relevance for regional climate shifts, such as a period of enhanced precipitation over Saharan Africa during the mid-Holocene. Here we present a theory for regional tropical rainfall shifts that utilizes both zonal and meridional energy fluxes. We first identify a qualitative link between zonal and meridional energy fluxes and rainfall variations associated with the seasonal cycle and the El Niño/Southern Oscillation. We then develop a quantitative theory based on these fluxes that relates atmospheric energy transport to tropical rainfall. When applied to the orbital configuration of the mid-Holocene, our theory predicts continental rainfall shifts over Africa and Southeast Asia that are consistent with complex model simulations. However, the predicted rainfall over the Sahara is not sufficient to sustain vegetation at a level seen in the palaeo-record, which instead requires an additional large energy source such as that due to reductions in Saharan surface albedo. We thus conclude that additional feedbacks, such as those involving changes in vegetation or soil type, are required to explain changes in rainfall over Africa during the mid-Holocene.
A taxonomic revision of the genus Polypogon Desf. s.1. (incl. Chaetotropis) in Chile was made. Eleven species and two varieties of Polypogon are recognized. Three new combinations are proposed [Polypogon elongatus Kunth var. longcaristatus (Nicora) Finot, P. exasperatus (Trin.) Renvoize var. kuntzei (Mez) Finot and P. magellanicus (Lam.) Finot]. Polypogon cachinalensis Phil, and P. elongatus var. strictus E. Desv. were revalidated. Polypogon purpurascens Phil, is considered a synonym of P. inferruptus Kunth, not of P. australis Brongn., and P. affinis Brong. moves to the synonymy of P. elongatus as was originally proposed by Desvaux (1854). Lectotypes of Agrostis exasperate Trin. var. purpurascens Kuntze, A. pectinata Hack. & Arechav, A. tehuclcha Speg., Polypogon rioplatensis Herter f. elegans Herter and P. longi/Jorus Nees ex Trin. are designated. The distribution of P. auslralis was extended to the Region of Arica and Parinacota and P. chilensis to the Region of Atacama. The presence of P. maritimus Willd. in Chile is rejected. Descriptions, synonymy, illustrations, specimens examined, and a key to species recognition are given.
Bouteloua (Poaceae: Chloridoideae: Cynodonteae; Boutelouiane) is an important genus of forage grasses containing 60 species found primarily in the Americas with a center of diversity in northern Mexico. A modern subgeneric classification is lacking. The goals of our study were to reconstruct the evolutionary history among the species of Bouteloua using molecular data with increased species sampling compared to previous studies. A phylogenetic analysis was conducted on 209 samples, of which 59 species (206 individuals) were in Bouteloua, using two plastid (rpl32-trnL spacer and rps16-trnK spacer) and nuclear ITS 1&2 (ribosomal internal transcribed spacer) sequences to infer evolutionary relationships and produce a subgeneric classification. Overall, ITS and plastid phylogenies rendered similar patterns. However, the ITS phylogeny lacked backbone structure, recovering only four internal clades out of nine found in the plastid phylogeny. The ITS network shows a radiative evolutionary pattern and indicates a number of incompatible splits, suggesting past hybridization between species of different sections. The maximum-likelihood tree from the combined plastid and ITS regions is well resolved and depicts a strongly supported monophyletic Bouteloua that includes ten strongly supported clades and one moderately supported clade. The molecular results support the recognition of 10 sections and two subsections within Bouteloua s.l.; three sections are new: Barbata, Hirsuta, and Trifida; four sections are new combinations: Buchloe, Cyclostachya, Opizia, and Triplathera; and two subsections are new: Eriopoda and Hirsuta. Based on our molecular results and the possession of unique morphological characters we describe a new species from Nuevo León, Bouteloua herrera-arrietae.
Nine diallelic nuclear microsatellite loci were characterized and developed as markers for analyses of diversity and population biology in creeping bentgrass, Agrostis stolonifera L. (2n = 4x = 28, A(2)A(2)A(3)A(3)). They may also help with identification of bentgrass germplasm resources. Polymorphic loci were isolated from genomic libraries from A. stolonifera and from A. transcaspica Litv. (2n = 2x = 14, putative A(3)A(3)). Markers were characterized in 87 A. stolonifera individuals from six distinct population sources. Analysis of molecular variance indicated significant variation between crop and wild groups. Highly significant variation was observed among and within the six populations. Bayesian analyses with STRUCTURE resolved crop from wild genotypes and assigned individuals to clusters that corresponded to their sources, in agreement with principal coordinates analysis results. The markers also correctly identified intraspecific creeping bentgrass F(1) hybrids. Cross-species analyses were conducted on sexually compatible relatives A. gigantea R. (2n = 6x = 42, A(1)A(1)A(2)A(2)A(3)A(3)), A. capillaris L. (2n = 4x = 28, A(1)A(1)A(2)A(2)), and A. canina L. (2n = 2x = 14, A(1)A(1) or possibly A(2)A(2)), plus A. transcaspica. Seven markers were diallelic in A. gigantea. Six of these markers were also diallelic in A. transcaspica, but not other species, suggesting that these loci are A(3) genome specific. Results also support the hypothesis that A. transcaspica is the source of the A(3) subgenome found in A. stolonifera and A. gigantea.
The subtribe Eleusininae (Poaceae: Chloridoideae: Cynodonteae) is a diverse group containing about 212 species in 31 genera found primarily in low latitudes in Africa, Asia, Australia, and the Americas, and the classification among these genera and species is poorly understood. Therefore, we investigated the following 28 Eleusininae genera: Acrachne, Afrotrichloris, Apochiton, Astrebla, Austrochloris, Brachyachne, Chloris, Chrysochloa, Coelachyrum, Cynodon, Daknopholis, Dinebra, Diplachne, Disakisperma, Eleusine, Enteropogon, Eustachys, Harpochloa, Leptochloa, Lepturus, Lintonia, Microchloa, Ochthochloa, Oxychloris, Saugetia, Schoenefeldia, Stapfochloa, and Tetrapogon. The goals of our study were to reconstruct the evolutionary history of the subtribe Eleusininae using molecular data with increased species sampling compared to earlier studies. A phylogenetic analysis was conducted on 402 samples, of which 148 species (342 individuals) were in the Eleusininae, using four plastid (rpl32-trnL spacer, ndhA intron, rps16-trnK spacer, rps16 intron) and nuclear ITS 1 & 2 (ribosomal internal transcribed spacer) sequences to infer evolutionary relationships and revise the classification. We found strong support for the following Eleusininae lineages: Acrachne, Apochiton, Astrebla, Austrochloris, Chloris, Chrysochloa, Cynodon, Daknopholis, Dinebra, Diplachne, Disakisperma, Eleusine, Enteropogon, Eustachys, Leptochloa, Lepturus, Micrachne gen. nov., Stapfochloa, and Tetrapogon, and moderate support for Harpochloa and Microchloa. Four species of Brachyachne, including the type, are imbedded within Cynodon; Oxychloris scariosa (monotypic) is sister to Harpochloa-Microchloa; Coelachyrum is polyphyletic since C. lagopoides, Apochiton burttii, and C. poiflorum form a grade, with the latter species sister to Eleusine; Schoenefeldia appears paraphyletic since Afrotrichloris martinii and Schoenefeldia transiens together are sister to Schoenefeldia gracilis; Saugetia fasciculata, Enteropogon brandegeei, and E. chlorideus are embedded within Tetrapogon; Lintonia nutans and Ochthochloa compressa are embedded in Chloris; and Enteropogon mollis and Chloris exilis are embedded in Leptochloa. Our plastid and ITS analyses show rearrangement of lineages within Acrachne and Chloris, indicating possible hybridization events or evidence for multiple origins. The molecular results support recognition of a new genus, Micrachne with five species and emendation of Stapfochloa with six species. We provide 22 new combinations, Chloris flagellifera, Ch. nutans, Cynodon ambiguus, C. prostratus, Diplachne divaricatissima, Leptochloa anisopoda, L. exilis, Micrachne fulva, M. obtusiflora, M. patentiflora, M. pilosa, M. simonii, Stapfochloa berroi, S. canterae, S. ciliata, S. elata, S. parvispicula, Tetrapogon brandegeei, T. chlorideus, T. fasciculatus, T. pleistachyus, and T. roxburghiana; a new name, Cynodon simonii; and lectotypify Eleusine flagillifera.
Based on recent molecular and morphological studies we present a modern worldwide phylogenetic classification of the ±12,074 grasses and place the 771 grass genera into 12 subfamilies (Anomochlooideae, Aristidoideae, Arundinoideae, Bambusoideae, Chloridoideae, Danthonioideae, Micraioideae, Oryzoideae, Panicoideae, Pharoideae, Puelioideae, and Pooideae), six supertribes (Andropogonodae, Arundinarodae, Bambusodae, Panicodae, Poodae, Triticodae), 52 tribes (Ampelodesmeae, Andropogoneae, Anomochloeae, Aristideae, Arundinarieae, Arundineae, Arundinelleae, Atractocarpeae, Bambuseae, Brachyelytreae, Brachypodieae, Bromeae, Brylkinieae, Centotheceae, Centropodieae, Chasmanthieae, Cynodonteae, Cyperochloeae, Danthonieae, Diarrheneae, Ehrharteae, Eragrostideae, Eriachneae, Guaduellieae, Gynerieae, Hubbardieae, Isachneae, Littledaleae, Lygeeae, Meliceae, Micraireae, Molinieae, Nardeae, Olyreae, Oryzeae, Oryzoideae, Paniceae, Paspaleae, Phaenospermateae, Phareae, Phyllorachideae, Poeae, Steyermarkochloeae, Stipeae, Streptochaeteae, Streptogyneae, Thysanolaeneae, Triraphideae, Tristachyideae, Triticeae, Zeugiteae, and Zoysieae), and 81 subtribes (Aeluropodinae, Agrostidinae, Airinae, Ammochloinae, Andropogoninae, Anthephorinae, Anthistiriinae, Anthoxanthinae, Arthraxoninae, Arthropogoninae, Arthrostylidiinae, Aveninae, Bambusinae, Boivinellinae, Boutelouinae, Brizinae, Buergersiochloinae, Calothecinae, Cenchrinae, Chionachninae, Chusqueinae, Coicinae, Coleanthinae, Cotteinae, Cteniinae, Cynosurinae, Dactylidinae, Dichantheliinae, Dimeriinae, Duthieinae, Eleusininae, Eragrostidinae, Farragininae, Germainiinae, Gouiniinae, Guaduinae, Gymnopogoninae, Hickeliinae, Hilariinae, Holcinae, Hordeinae, Ischaeminae, Loliinae, Melinidinae, Melocanninae, Miliinae, Monanthochloinae, Muhlenbergiinae, Neurachninae, Olyrinae, Orcuttiinae, Oryzinae, Otachyriinae, Panicinae, Pappophorinae, Parapholiinae, Parianinae, Paspalinae, Perotidinae, Phalaridinae, Poinae, Racemobambosinae, Rottboelliinae, Saccharinae, Scleropogoninae, Scolochloinae, Sesleriinae, Sorghinae, Sporobolinae, Stipinae, Torreyochloinae, Traginae, Trichoneurinae, Triodiinae, Tripogoninae, Tripsacinae, Triraphidinae, Triticinae, Unioliinae, Zizaniinae, and Zoysiinae). In addition, we include a radial tree illustrating the hierarchical relationships among the subtribes, tribes, and subfamilies. We use the subfamilial name, Oryzoideae, over Ehrhartoideae because the latter was initially published as a misplaced rank, and we circumscribe Molinieae to include 13 Arundinoideae genera. The subtribe Calothecinae is newly described and the tribe Littledaleeae is new at that rank.
The grass subtribe Sporobolinae contains six genera: Calamovilfa (5 spp. endemic to North America), Crypsis (10 spp. endemic to Asia and Africa), Psilolemma (1 sp. endemic to Africa), Spartina (17 spp. centered in North America), Sporobolus (186 spp. distributed worldwide), and Thellungia (1 sp. endemic to Australia). Most species in this subtribe have spikelets with a single floret, 1-veined (occasionally 3 or more) lemmas, a ciliate membrane or line of hairs for a ligule, and fruits with free pericarps (modified caryopses). Phylogenetic analyses were conducted on 177 species (281 samples), of which 145 species were in the Sporobolinae, using sequence data from four plastid regions (rpl32-trnL spacer, ndhA intron, rps16-trnK spacer, rps16 intron) and the nuclear ribosomal internal transcribed spacer regions (ITS) to infer evolutionary relationships and provide an evolutionary framework on which to revise the classification. The phylogenetic analysis provides weak to moderate support for a paraphyletic Sporobolus that includes Calamovilfa, Crypsis, Spartina, and Thellungia. In the combined plastid tree, Psilolemma jaegeri is sister to a trichotomy that includes an unsupported Urochondra-Zoysia clade (subtr. Zoysiinae), a strongly supported Sporobolus somalensis lineage, and a weakly supported Sporobolus s.l. lineage. In the ITS tree the Zoysiinae is sister to a highly supported Sporobolinae in which a Psilolemma jaegeri–Sporobolus somalensis clade is sister to the remaining species of Sporobolus s.l. Within Sporobolus s.l. the nuclear and plastid analyses identify the same 16 major clades of which 11 are strongly supported in the ITS tree and 12 are strongly supported in the combined plastid tree. The positions of three of these clades representing proposed sections Crypsis, Fimbriatae, and Triachyrum are discordant in the nuclear and plastid trees, indicating their origins may involve hybridization. Seven species fall outside the major clades in both trees, and the placement of ten species of Sporobolus are discordant in the nuclear and plastid trees. We propose incorporating Calamovilfa, Crypsis, Spartina, Thellungia, and Eragrostis megalosperma within Sporobolus, and make the requisite 35 new combinations or new names. The molecular results support the recognition of 11 sections and 11 subsections within Sporobolus s.l.; four sections are new: Airoides, Clandestini, Cryptandri, and Pyramidati; three sections are new combinations: Calamovilfa, Crypsis, and Spartina; four subsections are new combinations: Calamovilfa, Crypsis, Ponceletia, and Spartina; seven subsections are new: Actinocladi, Alterniflori, Floridani, Helvoli, Pyramidati, Spicati, and Subulati; 30 new combinations in Sporobolus: S. aculeatus, S. advenus, S. alopecuroides, S. alterniflorus, S. angelicus, S. arcuatus, S. bakeri, S. borszczowii subsp. acuminatus, S. borszczowii subsp. ambiguus, S. brevipilis, S. coarctatus, S. cynosuroides, S. densiflorus, S. factorovskyi, S. foliosus, S. hadjikyriakou, S. ×longispinus, S. maritimus, S. megalospermus, S. michauxianus, S. minuartioides, S. niliacus, S. pumilus, S. rigidus, S. rigidus var. magnus, S. spartinus, S. schoenoides, S. ×townsendii, S. turkestanicus, and S. vericolor; and five new names in Sporobolus: S. arenicola, S. ×eatonianus, S. hookerianus, S. mobberleyanus, and S. vaseyi are made. Lectotypes are designated for Crypsis factorovskyi, Heleochloa ambigua, and Torgesia minuartioides.
In phylogenomics the analysis of concatenated gene alignments, the so-called supermatrix, is commonly accompanied by the assumption
of partition models. Under such models each gene, or more generally partition, is allowed to evolve under its own evolutionary
model. Though partition models provide a more comprehensive analysis of supermatrices, missing data may hamper the tree search
algorithms due to the existence of phylogenetic (partial) terraces. Here we introduce the phylogenetic terrace aware (PTA)
data structure for the efficient analysis under partition models. In the presence of missing data PTA exploits (partial) terraces
and induced partition trees to save computation time. We show that an implementation of PTA in IQ-TREE leads to a substantial
speedup of up to 4.5 and 8 times compared with the standard IQ-TREE and RAxML implementations, respectively. PTA is generally
applicable to all types of partition models and common topological rearrangements thus can be employed by all phylogenomic
inference software.
We conducted a molecular phylogenetic study of the tribe Stipeae using nine plastid DNA sequences (trnK-matK, matK, trnH-psbA, trnL-F, rps3, ndhF, rpl32-trnL, rps16-trnK, rps16 intron), the nuclear ITS DNA regions, and micromorphological characters from the lemma surface. Our large original dataset includes 156 accessions representing 139 species of Stipeae representing all genera currently placed in the tribe. The maximum likelihood and Bayesian analyses of DNA sequences provide strong support for the monophyly of Stipeae; including, in phylogenetic order, Macrochloa as remote sister lineage to all other Stipeae, then a primary stepwise divergence of three deep lineages with a saw-like (SL) lemma epidermal pattern (a plesiomorphic state). The next split is between a lineage (SL1) which bifurcates into separate Eurasian and American clades, and a lineage of three parts; a small Patis (SL2) clade, as sister to Piptatherum s.str. (SL3), and the achnatheroid clade (AC). The AC exhibits a maize-like lemma
There is no easy way to identify to species, a small, vegetative leaf or culm sample of a grass and there are more than 12,000 species in this large, important family. The long-range aim of our study is to produce a standard DNA barcode library available to the public for all grasses (±1960 species) in North America (includes all Canada, Mexico and USA) that will facilitate the easy identification of these morphologically cryptic species. We provide a detailed protocol of the laboratory procedures for DNA extraction in grasses and the DNA-specific primers used for the polymerase chain reaction (PCR) enabling the laboratory work to be performed in any well-supplied molecular laboratory. In this paper we present a test of four barcodes [matK, rbcL, rpl32-trnL and internal transcribed spacer (ITS)] to discriminate among 50 taxa of grasses (55 samples), predominately in the subfamily Chloridoideae, and we used a tree-based method to identify relationships among species of Leptochloa sensu lato. The sequence divergence or discriminatory power based on uncorrected p-value, among the four DNA sequence markers was greatest in ITS (96%), followed by rpl32-trnL (25.6%), matK (3.0%) and rbcL (0.0%). matK was twice as effective in discriminating among the species compared with rbcL; rpl32-trnL was nearly 3.4 times better than rbcL; and nuclear rDNA ITS was 14 times better than rbcL. There are significant threshold levels of 0.0682 for ITS and 0.0732 for ITS + rpl32-trnL between intrageneric and intergeneric sequence divergences within the 16 species of Dinebra and between Dinebra and Diplachne, Disakisperma and Leptochloa sensu stricto. In our tree-based analyses of Leptochloa s.l. the following number of nodes with strong support (PP = 0.95−1.00) were successfully recovered (in descending order): combined ITS + rpl32-trnL, 43; ITS, 34; rp32-trnL, 27; matK, 19; and rbcL, 3.
Genetic interchange between American and Eurasian species is fundamental to our understanding of the biogeographical patterns, and we make a first attempt to reconstruct the evolutionary events in East Asia that lead to the origin and dispersal of two genera, Patis and Ptilagrostis. We conducted a molecular phylogenetic study of 78 species in the tribe Stipeae using four plastid DNA sequences (ndhF, rpl32-trnL, rps16-trnK, and rps16 intron) and two nuclear DNA sequences (ITS and At103). We use single copy nDNA gene At103 for the first time in the grasses to elucidate the evolutionary history among members of the Stipeae. Ampelodesmos, Hesperostipa, Oryzopsis, Pappostipa, Patis, and Stipa are found to be of multiple origins. Our phylograms reveal conflicting positions for Ptilagrostis alpina and Pt. porteri that form a clade with Patis coreana, P. obtusa, and P. racemosa in the combined plastid tree but are aligned with other members of Ptilagrostis in the ITS tree. We hypothesize that Ptilagrostis still retains the nucleotype of an extinct genus which transited the Bering land bridge from American origins in the late Miocene (minimum 7.35 to 6.37 mya) followed by hybridization and two plastid capture events with a Trikeraia-like taxon (7.96 mya) and para-Patis (between 5.32 to 3.76 mya). Ptilagrostis porteri and Patis racemosa then migrated to continental North America 1.7-2.9 mya and 4.3-5.3 mya, respectively.
A taxonomic revision of the genus Podagrostis (Griseb.) Scribn. & Merr. is presented, including two new combinations: P. meridensis (Luces) A. M. Molina & Rúgolo and P. novogaliciana (McVaugh) A. M. Molina & Rúgolo. Podagrostis bacillata (Hack.) Sylvester & Soreng constitutes a new report for Colombia. Information regarding synonymy, geographical distribution, habitat, iconography, and vernacular names is provided along with complete illustrations and a list of additional specimens examined. A key for the identification of the species is included as well as a comparative table based on macro- and micromorphological data. The anatomical character of Trichodium net on lemma epidermis, as well as its diagnostic value, is discussed in species of Podagrostis and most related genera (e.g., Agrostis L., Chaetotropis Kunth, and Polypogon Desf., among others).
Chascolytrum, as currently circumscribed, includes 22–23 South American species that were previously included in nine different genera (Chascolytrum, Briza, Poidium, Calotheca, Microbriza, Gymnachne, Rhombolytrum, Lombardochloa and Erianthecium). Due to the remarkable morphological diversity, the relationships in Chascolytrum s.l. have remained poorly understood, and no infrageneric classification could be proposed based on the latest molecular phylogenetic studies. In this study, we combined molecular (GBSSI, trnL-trnL-trnF and rps16 intron) and morphological characters to investigate the phylogenetic relationships in Chascolytrum s.l. Based on this, morphologically diagnosable clades were recognized as eight sections (Calotheca, Chascolytrum, Hildaea, Lombardochloa, Microbriza, Obovatae, Poidium and Tricholemma), of which three are new and three are monospecific. We describe each section and discuss the new infrageneric classification in comparison with the previous infrageneric classification proposed for the group under the genus Briza. A taxonomic key and images for most of the species in each section are provided. Last, the use of single-copy nuclear genes and morphological data for future phylogenetic reconstructions encompassing Chascolytrum is highlighted.
This thesis explores the potential influence of a range of biological mechanisms (polyploidy, breeding system and edaphic adaptation - salinity tolerance) on diversification of Lachnagrostis Trin.(Poaceae): a largely Australian and New Zealand genus, with a few South African and South American taxa, recently segregated from Agrostis L. The genus occurs across a wide range of temperate environments from coastal to montane conditions, from grassland to forest and from non-saline to saline soils. Morphological differences between some taxa are subtle but nevertheless distinct and have led to the ongoing recognition of new species. The relationship between Lachnagrostis and other members of the subtribe Agrostidinae was examined through the construction of a phylogeny based on the cpDNA regions, rbcL and matK and the nDNA region, ITS, derived from sampling and sequencing herbaria collections in order to answer i) whether or not Lachnagrostis should be regarded as a genus in its own right, ii) whether the non-Australasian taxa are part of a Lachnagrostis clade and if so, with which Australasian species they are most closely related and iii) whether a phylogenetic signal exists within Lachnagrostis that could provide clues to historical or contemporary speciation events. Sequencing was supplemented with an AFLP analysis of the majority of Lachnagrostis taxa to provide an enhanced phylogeny of the genus. Polyploidy was examined through determination of C-values across a range of nursery grown populations and thumb-squash chromosome counts on selected examples. Breeding system was examined through nursery observations of the timing of anther dehiscence in relation to anthesis. Salinity tolerance was examined through the measurement of seed germination and plumule and radicle response. The distribution of each trait was examined across a broad range of taxa and populations and the potential of each interpreted against the phylogenetic relationship amongst taxa. None of the DNA regions proved to be variable enough to provide a fully resolved phylogeny at either the subtribe or genus level, although subtribal relationship inferences were greatly improved when the three regions were combined. Phylogenetic analysis did not support a monophyly for Lachnagrostis and in particular, split the NZ taxa between two clades. The AFLP analysis provided better taxonomic definition within the genus but backbone support for a robust phylogeny was again lacking. These lines of evidence suggest incomplete lineage sorting and recent, and in some cases contemporaneous diversification within the genus: probably linked to increasing landscape fragmentation. High-level polyploidy is the norm within Lachnagrostis but is poorly correlated with C-value. Among taxa with the highest C-values were the perennial L. billardierei and the highly salt-tolerant L: adamsonii and L. robusta while the lowest C-value and chromosome counts were found for L. punicea: a sister taxon of the Australian clade. Inbreeding appears to be common, even in widespread species and suggests inflorescence dispersal as a major mechanism for gene flow between populations. A high degree of salt tolerance, even among taxa normally growing in non-saline environments suggests that adaptation to salinity is as much a response to phenotypic plasticity as to natural selection.
Three South African Agrostis L. taxa are transferred to Lachnagrostis Trin., as L. eriantha (Hack.) A.J.Br., L. huttoniae (Hack.) A.J.Br. and L. polypogonoides (Stapf) A.J.Br. on the basis of high palea to lemma length ratios and a lack of a trichodium net pattern on the lemma epidermis. However, the lemmas of L. barbuligera var. barbuligera and A. barbuligera var. longipilosa Gooss. & Papendorf have a trichodium net and do not belong in Lachnagrostis. Instead, they are morphologically similar to a group of montane tropical African Agrostis, which includes A. kilimandscharica Mez. and A. mannii (Hook.f.) Stapf. Previous transfers of A. griquensis Stapf and A. viridis Gouan to Polypogon are confirmed as appropriate, as they lack a trichodium net but, unlike Agrostis and Lachnagrostis, their spikelets disarticulate below the glumes.
Genetic relationships among Agrostis species used for turf have been difficult to discern. Recent studies have either confirmed or contradicted previously proposed genetic relationships based on chromosome pairing behavior of inter-specific hybrids. The objective of the current study was to assess genetic relationships among Agrostis cultivars and accessions by using newly available A. stolonifera microsatellite (SSR) markers. Nuclear SSR (nuSSR) and chloroplast SSR (cpSSR) markers were used to genotype 16 individuals from each of 74 Agrostis cultivars and accessions. Genetic relationships based on nuSSR markers most closely resembled species relationships proposed by Jones in the 1950s. Contrary to the work of Jones, genetic relationships based on cpSSR markers indicated that A. canina was more closely related to A. stolonifera than to A. capillaris. We hypothesize that chloroplast introgression via interspecific hybridization between A. canina and A. stolonifera resulted in these species sharing common chloroplast genome lineages, while maintaining disparate nuclear genome lineages. Genetic relationships within Agrostis species based on nuSSR markers closely matched known pedigree relationships. Bayesian clustering analysis of nuSSR markers indicated that most modern seeded A. stolonifera cultivars exhibited high levels of admixture. Our study confirms that nuSSR markers distinguish Agrostis species and cultivars, and are valuable for studying genetic diversity and genetic relationships within the genus Agrostis.
Many early reports of ITS region (ITS 1, 5.8S, and ITS 2) variation in flowering plants indicated that nrDNA arrays within individuals are homogeneous. However, both older and more recent studies have found intra-individual nrDNA polymorphism across a range of plant taxa including presumed non-hybrid diploids. In addition, polymorphic individuals often contain potentially non-functional nrDNA copies (pseudogenes). These findings suggest that complete concerted evolution should not be assumed when embarking on phylogenetic studies using nrDNA sequences. Here we (1) discuss paralogy in relation to species tree reconstruction and conclude that a priori determinations of orthology and paralogy of nrDNA sequences should not be made based on the functionality or lack of functionality of those sequences; (2) discuss why systematists might be particularly interested in identifying and including pseudogene sequences as a test of gene tree sampling; (3) examine the various definitions and characterizations of nrDNA pseudogenes as well as the relative merits and limitations of a subset of pseudogene detection methods and conclude that nucleotide substitution patterns are particularly appropriate for the identification of putative nrDNA pseudogenes; and (4) present and discuss the advantages of a tree-based approach to identifying pseudogenes based on comparisons of sequence substitution patterns from putatively conserved (e.g., 5.8S) and less constrained (e.g., ITS 1 and ITS 2) regions. Application of this approach, through a method employing bootstrap hypothesis testing, and the issues discussed in the paper are illustrated through reanalysis of two previously published matrices. Given the apparent robustness of the test developed and the ease of carrying out percentile bootstrap hypothesis tests, we urge researchers to employ this statistical tool. While our discussion and examples concern the literature on plant systematics, the issues addressed are relevant to studies of nrDNA and other multicopy genes in other taxa.
In the mid-Holocene, the climate of northern Africa was characterized by wetter conditions than present, as evidenced by higher paleolake levels and pollen assemblages of savannah vegetation suggesting a wetter, greener Sahara. Previous modeling studies have struggled to simulate sufficient amounts of precipitation when considering orbital forcing alone, with limited improvement from considering the effects of local grasslands. Here it is proposed that remote forcing from expanded forest cover in Eurasia relative to today is capable of shifting the intertropical convergence zone northward, resulting in an enhancement in precipitation over northern Africa approximately 6000 years ago greater than that resulting from orbital forcing and local vegetation alone. It is demonstrated that the remote and local forcing of atmospheric circulation by vegetation can lead to different dynamical patterns with consequences for precipitation across the globe. These ecoclimate teleconnections represent the linkages between the land surface in different regions of the globe and by inference show that proxy records of plant cover represent not only the response of vegetation to local climate but also that vegetation's influence on global climate patterns.
Jacobs, S.W.L. (Royal Botanic Gardens, Sydney, NSW 2000, Australia) 2001 The genus Lachnagrostis (Gramineae) in Australia. Telopea 9(3): 439-448. Lemma epidermal features were examined in species of Agrostis, Deyeuxia and Calamagrostis. As a result the genus Lachnagrostis is recognised and new combinations provided for L. adamsonii, L. aequata, L. collicola, L. drummondiana, L. lacunis, L. limitanea, L. meionectes, L. punicea and L. robusta. A key distinguishing Lachnagrostis from the related genera Dichelachne, Deyeuxia, Agrostis is given, along with a characterisation of the four genera. Synonymy is provided for the other species of Lachnagrostis recognised in Australia. It is concluded that both Deyeuxia and Calamagrostis are diverse and highly variable and little is to be gained by combining them at this stage though their current circumscriptions are probably suboptimal.