trnL trnF Research Articles

One more species in the genus Jungermannia (Marchantiophyta: Jungermanniaceae)

Jungermannia afoninae is described from the mountains of South Siberia based on a complex taxonomical approach exploring critical reinvestigation of morphological features and analyses of newly obtained trnL–trnF and trnG-intron cpDNA sequences from six Jungermannia specimens incorporated into a previously published dataset. Description and illustrations of the new species are provided with notes on its differentiation from allied species, ecology and distribution.

Genetic diversity and demographic analysis of an endangered tree species Diplopanax stachyanthus in subtropical China: implications for conservation and management

With climatic change and anthropogenic activities, endangered species in subtropical China face high risk of extinction. However, many of them have received little attention in the past. In this study, three chloroplast DNA fragments (trnL–trnF, trnH–psbA, rps16) and integrated species distribution models were employed to evaluate the genetic diversity, genetic structure and distribution area changes of the endangered tree species Diplopanax stachyanthus. We identified three lineages (i.e., the eastern, central and western lineages) and high levels of genetic diversity in this species. The genetic differentiation is extremely high among the three lineages and among populations; most of the ten populations fixed private haplotype(s). Our time estimation elucidated that the splits of these lineages occurred during Pliocene to Pleistocene. Bayesian skyline plots analyses showed the change of effective population size of D. stachyanthus at ca. 0.1 Ma. Multiple interglacial refugia were inferred for D. stachyanthus in subtropical China. Climatic fluctuation and geographic changes during the Quaternary as well as habitat losses may have played important roles in driving intraspecific divergence and shaped current genetic structure of D. stachyanthus. Furthermore, there may be a major decrease in the suitable habitats for this species. Our findings would shed light on the evolutionary history of D. stachyanthus in subtropical China, and facilitate the conservation and management of this species.

<p align="center">An unusual disjunction in Loasaceae: Central American Chichicaste grandis is nested in Brazilian Aosa

The highly distinctive genus Chichicaste is restricted to the Costa Rica-Chocó Biogeographic Hotspsot from Costa Rica to northwestern Colombia and comprises a single species, C. grandis. Relationships of this taxon have been doubtful in the absence of critical morphological analyses (particularly of living plants) and convincing molecular data. The present study aims at identifying the phylogenetic relationships of C. grandis using molecular and morphological data to establish its relationships. Our molecular data set includes four plastid markers (trnL–trnF, matK, trnS–trnG and rps16) and the nuclear marker ITS for 38 in-group taxa, including all of the currently recognized genera of the Loasoideae clade, and six out-group taxa from non Loasoideae Loasaceae and Hydrangeaceae. The dataset was analyzed using Maximum Likelihood and Bayesian Inference approaches. The plastid and nuclear trees were mostly congruent, with their respective ML best and BI strict consensus trees showing no significant differences in their topologies. Chichicaste is nested in Aosa series Parviflorae and sister to A. plumieri from Hispaniola, thus representing northern and western outliers of this otherwise strictly Brazilian genus. A critical morphological re-examination indicates that considering C. grandis as part of Aosa is plausible, in spite of the ecological and morphological differences between the two taxa. Based on these results the genus Chichicaste is synonymized with Aosa and the required new combination is provided. An amended key for an expanded Aosa, is also presented.

Intergeneric relationships in the Gorteria clade of Arctotideae-Gorteriinae (Asteraceae), with description of a new genus, Roessleria

Previous phylogenetic studies in the Arctotideae-Gorteriinae (Asteraceae) have found support for a Gorteria clade. The results also indicated Hirpicium to be paraphyletic, whereas Gorteria and Gazania were found to be monophyletic. Previous investigations at the genus level on this group have focused only on relationships in Gazania and Gorteria, respectively, with only a few Hirpicium species included. In the present study we include more taxa than in any previous investigation, including all species of Hirpicium, all species of Gorteria and almost all taxa of Gazania. Phylogenetic analyses, based on DNA sequence data from non-coding (rps16, trnL–trnF, and psbA–trnH) as well as coding (ndhF) regions from the plastid genome resolved three major clades, but DNA sequence data from the ribosomal regions (ETS and ITS) from the nuclear genome did not support two of the three clades. The genus Hirpicium, as presently circumscribed, was paraphyletic with one group of four species nested within Gorteria and all remaining species of Hirpicium formed a monophyletic group with two clades, morphologically well-defined. As the name Hirpicium is a synonym of Gorteria, new names for the remaining Hirpicium species are proposed. For one of the Hirpicium clades, comprising Hirpicium echinus, we resurrect the genus Berkheyopsis O. Hoffm., and for the five species belonging to the second clade a new generic name, Roessleria Stångb. & Anderb., is proposed. The necessary new combinations, 12 in total, are made, as well as four lectotypifications and one neotypification. A key to the newly circumscribed genera is presented.

Modern State of Populations of Endemic Oxytropis Species from Baikal Siberia and Their Phylogenetic Relationships Based on Chloroplast DNA Markers

The genetic diversity and population structure of the endemic species of Baikal Siberia Oxytropis triphylla, O. bargusinensis, and O. interposita were studied for the first time on the basis of the nucleotide polymorphism of intergenic spacers psbA–trnH, trnL–trnF, and trnS–trnG of chloroplast DNA. All populations of these species were characterized by a high haplotype (0.762–0.924) and relatively low nucleotide (0.0011–0.0022) diversity. Analysis of the distribution of variability in O. triphylla and O. bargusinensis showed that there was no significant genetic differentiation between populations of each species; the gene flow was 4.43 and 8.91, respectively. The high level of genetic diversity in the studied populations indicates a relatively stable state of these populations. A study of the phylogenetic relationships of closely related species confirms the concept of the origin of O. bargusinensis and O. tompudae as a result of intersectional hybridization of the species of the sections Orobia and Verticillares.

Phylogenetic relationships among Ananas and related taxa (Bromelioideae, Bromeliaceae) based on nuclear, plastid and AFLP data

Since the first description of the genus in 1754, the taxonomy of Ananas underwent many fundamental changes and it is still the subject of a vivid debate. We present a phylogeny comprising all seven known Ananas taxa, Pseudananas sagenarius as well as closely related members of Bromelioideae (Aechmea subg. Chevaliera) based on three nuclear markers (agt1, ETS, phyC), five plastid markers (atpB–rbcL, trnL–trnF, matK, two segments of ycf1) and AFLP data. This study reveals a close relationship between Ananas, P. sagenarius, Aechmea tayoensis and Disteganthus basilateralis, and proposes novel relationship of the Ananas clade and Aechmea fernandae. Taxonomic implications of our analysis in particular the recognition of species versus varieties in Ananas are discussed. Furthermore, we could show that the evolution of two traits (scape bracts and the apical coma of the inflorescence) might be interlinked.

Home at last III: Transferring Uechtritzia and Asian Gerbera species into Oreoseris (Compositae, Mutisieae).

Recently the Asian Gerbera species were shown to form a clade that was not the sister group of the African Gerbera. In this study, the position of the Asian Gerbera species was further assessed based on morphology and molecular phylogenetic analyses that included six Asian Gerbera and 26 other species from the Gerbera-complex. Morphological results showed that the six Asian Gerbera species, which were sampled, bear leaves with the adaxial epidermal surface lacking stomates, possess bracteate scapes and lack inner ray florets. These characters suggest that the Asian Gerbera species are most closely related to the species of Uechtritzia, which also share similar pollen grain size and shape with the Asian Gerbera, rather than to the African Gerbera. Furthermore, the phylogenetic results based on two nuclear (ITS and ETS) and three chloroplast (trnL–trnF, trnL–rpl32 and trnC–petN) sequences strongly support the Asian Gerbera and Uechtritzia forming a clade, with the latter nested within the Asian Gerbera species. Both morphological and molecular phylogenetic data thus confirmed the taxonomic identity of the Asian Gerbera and Uechtritzia. The authors herein formally treat the nine species of the Asian Gerbera and the three species of Uechtritzia as members of the genus Oreoseris, which is the earliest generic name of this lineage and has the nomenclatural priority.

Molecular systematics of Caryopteris (Lamiaceae) and its allies with reference to the molecular phylogeny of subfamily Ajugoideae

AbstractAjugoideae, the third–largest subfamily of Lamiaceae with 23 genera and about 760 species, is distributed worldwide, but is primarily found in tropical regions. During the past two decades, substantial progress has been made towards discerning phylogenetic relationships and generic boundaries in Ajugoideae, but major questions still remain. This phylogenetic study was conducted using 422 DNA sequences from seven DNA regions (nrITS, ETS, and matK, rbcL, rps16, trnL–trnF, trnH–psbA) representing 50 species from 22 of 23 genera in Ajugoideae, to reconstruct the backbone phylogeny of the subfamily, with emphasis on phylogenetic relationships among Caryopteris, Schnabelia and their closest allies. Key results: (1) Ajugoideae is monophyletic and can be divided into four main clades. (2) Discretitheca and Glossocarya, which have not been included in any previous molecular analysis, are members of Ajugoideae and closely related to Karomia and Rotheca. (3) Expanded Schnabelia is monophyletic, sister to Rubiteucris, and consists of two morphologically distinct clades, recognized here as sect. Cylindricaulis and sect. Schnabelia. (4) Traditionally defined Caryopteris is confirmed to be polyphyletic, with several segregate genera. (5) Recircumscribed Caryopteris was found to be monophyletic, but intrageneric relationships were not fully resolved. Synapomorphies of Caryopteris include boat–shaped nutlets that are winged along the edge, fimbriate anterior corolla lobes, and suprareticulate pollen sculpturing. Caryopteris forrestii var. minor was elevated to species rank based on molecular and morphological evidence.

Phylogeny of Zehneria (Cucurbitaceae) with special focus on Asia

AbstractZehneria is a genus of small creepers and climbers from the Old–World Tropics and Subtropics. In its broadest circumscription, it comprises up to 94 species and its centre of diversity is Southeast Asia. Zehneria has been split into several smaller genera but this remained controversial mainly due to morphological plasticity of the species groups and lack of comprehensive molecular data. Here, we use one nuclear DNA (ITS1–5.8S–ITS2) and three plastid DNA regions (trnL–trnF, rpl20–rps12, matK) sequenced for about half of the species in Zehneria and its segregate genera Anangia, Neoachmandra, and Pilogyne to test the monophyly of the genus and analyse the evolutionary history of the group. We find that Zehneria s.l. is monophyletic and splitting is not supported by molecular, morphological or biogeographical evidence. Within Zehneria, we recover two strongly supported clades, one consisting mainly of species placed in Pilogyne, the other including Anangia, Neoachmandra and the type of Zehneria. Both clades comprise African, Asian, and Australian/Pacific Island species, which is evidence for high dispersal capacity in this young bird–dispersed group. For India, we accept the five species Z. bodinieri, Z. hookeriana, Z. maysorensis, Z. odorata, and Z. thwaitesii. For Myanmar, we increase the number of known species from four to eight, including three still unnamed species. The diversity hotspots for the genus, however, remain Indonesia and Thailand with together 25 species.

Phylogenetic relationships and generic reassessment of Proustia and allies (Compositae: Nassauvieae)

AbstractProustia is a small southern Andean genus of shrubs, vines and small trees, which are characteristic elements of Chilean and Argentine Andean forests, thickets and desert scrubs. Since Proustia possesses an unusual and characteristic morphology within the Nassauvieae, its circumscription as well as its phylogenetic placement is decisive in understanding the evolution of the tribe. Berylsimpsonia, from the Caribbean, was segregated from Proustia, which currently only includes three species. Lophopappus, another Andean genus, has been closely related to Proustia in sharing style and corolla features that are unusual in the Nassauvieae. The purpose of this work is to evaluate the placement of Proustia within the Nassauvieae, its relationships with Berylsimpsonia and Lophopappus, and the relationships of its species using molecular data and phylogenetic methods. This is the first comprehensive analysis of Proustia. We have included in our study the three currently accepted species of Proustia and seven of its ten infraspecific taxa. For each taxon of Proustia, one to seven accessions were analyzed. Species of Lophopappus and Berylsimpsonia, as well as 16 species belonging to 13 genera of Nassauvieae were also analyzed. We sequenced the nuclear ribosomal ITS and ETS, and the plastid regions ndhF, 5’ trnK–matK, trnL–trnF, and trnL(UAG)–rpl32. Unlike other previous studies, Proustia is not sister to the rest but nested in the tribe in our analyses. Berylsimpsonia vanillosma and P. ilicifolia are distantly related to P. pyrifolia, the type of the genus. According to nuclear DNA data, the infraspecific taxa of P. cuneifolia were recovered all in a well–supported clade, although based on the plastid data P. pyrifolia does not form a lineage separate from P. cuneifolia. Lophopappus is the genus most closely related to Proustia. Regarding the evolution of styles, our results suggest multiple origins of atypical stylar features in the Nassauvieae. As a result of our analyses we propose the segregation of Proustia ilicifolia into the new genus Spinoliva. Morphological data are consistent with the segregation of Proustia and Lophopappus as separate genera. Two species of Proustia, P. cuneifolia and P. pyrifolia are recognized. Three lectotypifications, one neotypification, two new combinations and five rank changes are proposed.

The genealogy of geebungs: phylogenetic analysis of Persoonia (Proteaceae) and related genera in subfamily Persoonioideae

Proteaceae subfamily Persoonioideae, as presently circumscribed, consists of the monogeneric tribe Placospermeae (Placospermum) and the tribe Persoonieae. The latter comprises the diverse genus Persoonia and monospecific genera found in New Zealand (Toronia), New Caledonia (Garnieria) and south-western Western Australia (Acidonia). Persoonia has 101 species distributed across Australia and has been classified into 11 informal groups. Using data derived from plastid DNA (trnL–trnF region), nuclear rDNA (ITS) and morphological characters, we constructed a phylogeny of Persoonioideae and compared the results to the existing classification. Bayesian and parsimony analyses indicated that Persoonia, as currently defined, is non-monophyletic. The molecular data and combined molecular and morphological data place Toronia in a moderately well supported clade with the monophyletic Rufiflora group of Persoonia from Western Australia. This clade is sister to Acidonia, Garnieria and the remaining Persoonia species. Of the other informal groups in Persoonia, the Teretifolia, Quinquenervis, Laurina, Arborea, Graminea and Chapmaniana groups are supported as monophyletic. The Lanceolata group can be re-circumscribed to be monophyletic by the addition of P. elliptica R.Br. (Longifolia group) and the Dillwynioides group. Relationships within this large, geographically widespread clade are largely unresolved and low DNA-sequence variation within it suggests a recent radiation followed by isolation in south-western and eastern Australia. All endemic Tasmanian Persoonia (Gunnii group taxa) are unresolved at the second-most basal node of the Persoonieae. Our results suggest that the Rufiflora group should be treated as a new genus and that the infrageneric taxonomy of Persoonia requires minor amendment.

Molecular phylogeny of the genus Bolusiella (Orchidaceae, Angraecinae)

Recent molecular studies have suggested the monophyly of Bolusiella, a small orchid genus comprising five species and one subspecies from Continental Africa, but sampling has been limited. Using the species delimitation presented in the recent taxonomic revision of the genus, this study aimed to confirm the monophyly of Bolusiella and assess the interspecific relationships using a comprehensive sampling and various analytical methods. DNA sequences of one nuclear spacer region (ITS-1) and five plastid regions (matK, rps16, trnL–trnF, trnC–petN, and ycf1) from 20 specimens representing all five species of the genus were analyzed using static homology, dynamic homology, and Bayesian methods. The monophyly of both the genus Bolusiella and each of its five species was confirmed, corroborating the previously published taxonomic revision. The use of dynamic homology methods was not conclusive for this particular group. The results of the total evidence analysis (combining all six sequence regions) using the dynamic homology approach yielded a slightly different hypothesis regarding interspecific relationships (namely the exchange of B. talbotii and Bolusiella iridifolia as the earliest diverging lineage), probably because the nodes in question are supported by a small subset of conflicting characters, compared to the hypotheses resulting from the static homology and Bayesian methods, which are congruent with the results of previous studies.

Genetic variability of Eurasian Nuphar species unravels possible routes in which freshwater plants could fill their wide areas

Possible routes in which aquatic plants have spreaded across their vast ranges from ancestral areas and refugia still remain poorly known. We have chosen Eurasian yellow water-lilies (Nuphar Sm. sect. Nuphar, Nymphaeaceae) as a model group for a wide-scale phylogeographical study as they represent a common component of the continental freshwater flora. To elucidate the history of diversification of the section Nuphar, we sequenced nuclear ribosomal ITS and chloroplast intergenic spacers (trnH-psbA, trnL–trnF) from 117 localities from almost all the section area. Sequence data were analysed with a statistical parsimony approach using the network algorithm. We also incorporated data on morphological variation and pollen viability. The section Nuphar originated and diversified into several evolutionary lineages in Eastern Asia. Two lineages, represented by N. pumila and N. lutea, spread from the Russian Far East westwards to Siberia and further to Europe. Nuphar pumila also migrated from the Far East to North America (where it is referred to as N. microphylla). Nuphar lutea colonized deglaciated north-eastern Europe not only from the south, but also from the Siberian refugia. Nuphar lutea and N. pumila hybridize rarely in Eastern Europe and Asia and warrant species status. We provide the first evidence, based on a phylogeographical approach, for the origin and diversification of aquatic flowering plants in Eastern Asia. Our results indicate that phylogeographic analysis on the area-wide scale is one of the most efficient ways to deduce possible routes in which aquatic plants have spread across their total range from ancestral areas and refugia.

Weeding the nettles VI: Taxonomic and phylogenetic studies of the Southeast Asian Urtica fissa-clade (Urticaceae)

Urtica L. (Urticaceae) is a subcosmopolitan genus common throughout temperate Asia. Species delimitation is very difficult and the present study investigates a group of taxa associated with Urtica fissa from East-Southeast Asia and based mainly on herbarium collections, including most of the type specimens and cultivated plants. Species limits especially of U. mairei, U. fissa and U. himalayensis have been consistently confused in both herbaria and floristic treatments. As part of a taxonomic revision we produced a molecular phylogeny of the group based on ITS1-5.8S-ITS2, psbA–trnH, trnL–trnF and trnS–trnG markers. Our revision recovers a total of five species and two subspecies: U. fissa E.Pritz. ex Diels, U. grandidentata Miq. subsp. grandidentata, U. grandidentata Miq. subsp. lombok K.Becker & Weigend, U. himalayensis Kunth & C.D.Boché, U. mairei Lév. and U. parviflora Roxb. We provide type information, diagnostic characters, a key to species identification, species conservation assessments and a list of exsiccatae for each taxon.

Weeding the nettles V: Taxonomic and phylogenetic studies of the eastern Asian species Urtica thunbergiana Sieb. & Zucc. (Urticaceae)

Urtica L. (Urticaceae) is a subcosmopolitan genus, which is also common throughout Asia. Taxon differentiation in the Asian Urtica species is difficult due to the limited diversity of taxonomically useful characters combined with a range of phenotypic variation. The present study investigates the species Urtica thunbergiana Sieb. & Zucc. (incl. U. laetevirens) from eastern Asia based on herbarium collections, including most of the type specimens. The delimitation of U. thunbergiana is expanded to include all three currently recognized subspecies of U. laetevirens Maxim. Also, one newly infraspecific taxon is described from Taiwan. Based on our revision, the recognition of a total of four subspecies of Urtica thunbergiana is proposed: subsp. thunbergiana, subsp. dentata (Hand.-Mazz.) K.Becker & Weigend, subsp. silvatica (Hand.-Mazz.) K.Becker & Weigend, and subsp. perserrata, subspec. nov. The systematic re-arrangements are based on morphological analyses and a highly resolved phylogeny based on the molecular markers ITS1–5.8S–ITS2, psbA–trnH, trnL–trnF and trnS–trnG.

Bolanthus sandrasicus sp. nov. (Caryophyllaceae) from Turkey

Bolanthus sandrasicus Hamzaoğlu & Koç sp. nov. from the Muğla province, SW Turkey, is described. This new species resembles B. thymoides Hub.‐Mor., but differs in both macromorphology and seed micromorphology. Furthermore, we investigated the phylogenetic relationships of all Bolanthus species distributed in Turkey using ITS and trnL–trnF sequence data. The results of both morphological and molecular analyses support the description of the recently discovered Muğla population as a distinct species. In addition, a diagnostic key to all Bolanthus species growing in Turkey is provided.

Phylogeny of the Neotropical sages (Salvia subg. Calosphace; Lamiaceae) and insights into pollinator and area shifts

Salvia subg. Calosphace (Lamiaceae, Lamiales) is a highly diverse clade endemic to the New World. The phylogenetic relationships of Calosphace have been previously investigated using DNA sequences of nuclear ITS region and plastid psbA–trnH intergenic spacer, but the resulting trees lack resolution and support for many clades. The present paper reassesses the phylogenetic relationships of subgenus Calosphace, including a broader taxon sampling, with a special focus on representing previously unsampled sections, and using an additional plastid marker (trnL–trnF region). Our results show increased resolution and overall patterns of support, recovering ten main clades. Within core Calosphace, the most inclusive of these main clades, 17 new subclades were identified. Of the 42 sections for which more than one species was analysed, only 12 are monophyletic. Our biogeographical analysis identified at least twelve migrations to South America from Mexican and Central American lineages, in agreement with previous suggestions of multiple origins of South American Calosphace diversity. This analysis also confirmed a colonization of the Antilles by Andean lineages. The reconstruction of ancestral states of pollination syndromes showed multiple shifts to ornithophily from melittophily and one reversal to the latter.

Genetic diversity and population structure of Taxus cuspidata Sieb. et Zucc. ex Endl. (Taxaceae) in Russia according to data of the nucleotide polymorphism of intergenic spacers of the chloroplast genome

The genetic diversity and population structure of Taxus cuspidata Sieb. et Zucc. ex Endl. on the Russian part of its range was studied for the first time on the basis of the nucleotide polymorphism of intergenic spacers psbA–trnH, trnL–trnF, and trnS–trnfM of chloroplast DNA. A high level of gene (h = 0.807) and nucleotide (π = 0.0227) diversity was revealed. The data of AMOVA showed that the interpopulation component accounted for 12% of genetic variability (F ST = 0.12044, P = 0.0000). We revealed 15 haplotypes, four of which were shown to be unique. The presence of common haplotypes in the majority of populations, the absence of phylogenetic structure, and low values or even the absence of nucleotide divergence show that the T. cuspidata populations studied are fragments of the once common ancestor population. Geographical isolation, which resulted from climatic changes in the Pleistocene–Holocene, as well as from human activities, did not produce a significant effect on the genetic structure of the species.

Pseudoheterocaryum, a new genus segregated from Heterocaryum (Boraginaceae) on the basis of molecular data

The phylogeny of Heterocaryum and Suchtelenia was examined using sequence data from the internal transcribed spacer region of the nuclear rDNA (ITS) and plastid trnL intron and trnL–trnF intergenic spacer (trnL–F) regions. Results indicated that Heterocaryum is non-monophyletic because of the inclusion of Suchtelenia calycina (C.A.Mey.) A.DC. Heterocaryum laevigatum (Kar. & Kir.) A.DC. formed a distinct branch sister to S. calycina and remaining Heterocaryum species. Hence, all species of Heterocaryum except H. laevigatum (type species of the genus) are transferred to a new genus, Pseudoheterocaryum. Taxonomic descriptions are presented for Pseudoheterocaryum and Heterocaryum, as well as a diagnostic key to the three genera included in the present study.

Allium urusakiorum (Amaryllidaceae), a new member of the Balkan clade of the section Oreiprason from European Turkey

The taxonomy of the Allium saxatile group (sect. Oreiprason) has been studied recently upon morphological and molecular data. New specimens collected from the European part of Turkey near the Istranca Mountains and identified as ‘A. saxatile’ proved to be a new species confirmed by sequences of internal transcribed spacer (ITS) and two plastid DNA regions (rpl32–trnL and trnL–trnF) and supported by morphological characters. Allium urusakiorum, a new species from the A. saxatile group, is described here through living and herbarium specimens. It is the only species of the sect. Oreiprason in the country and seems to be an endemic species of the Turkish flora. Characteristics of the species include morphological description, identification key, molecular dataset, and karyotype (2n = 16).