What is the subtribe Glossonematinae (Apocynaceae: Asclepiadoideae)? A phylogenetic study based on cpDNA spacer

Evidence from the chloroplast trn T-L spacer, trn L intron and trn L-F spacer shows the subtribe Glossonematinae of the tribe Asclepiadeae, hitherto composed of the Arabian and North African genera Glossonema , Odontanthera and Solenostemma , not to be monophyletic. While the affinities of Solenostemma cannot be determined with certainty at present, molecular, karyological and morphological evidence suggests that Glossonema and Odontanthera are closely allied to Pentarrhinum , an African genus of five species, belonging to the Cynanchinae.  © 2002 The Linnean Society of London, Botanical Journal of the Linnean Society , 2002, 139 , 145–158.     

Molecular phylogeny of the genus Philodendron (Araceae): delimitation and infrageneric classification

The genus Philodendron (Araceae) is a large neotropical group whose classification remains unclear. Previous classifications are based on morphological characters, mainly from the inflorescence, flower and leaf shape. The classification by Krause, with few modifications, is still the most commonly used system. To examine phylogenetic relationships in the genus, two ribosomal DNA nuclear markers, internal transcribed spacer (ITS) and external transcribed spacer (ETS), and the chloroplast intron rpl 16, were sequenced and analysed for more than 80 species of Philodendron and its close relative Homalomena . According to the resulting phylogeny, the genus Homalomena may be paraphyletic to the genus Philodendron . The inclusion of the American Homalomena species within the genus Philodendron might resolve this taxonomic problem. All three subgenera of Philodendron were revealed as monophyletic. Below the subgeneric level, the groups obtained in our phylogeny globally correspond to sections recognized in previous classifications. Among the morphological characters used by previous taxonomists to build their classifications, and which we optimized onto one of the most parsimonious trees, most characters were found to be homoplasious. However, leaf shape, characteristics of the sterile zone on the spadix and venation patterns are useful for delimiting subgenera and sections within the genus.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 13–27.     

Geographical diversification of the genus Cicer (Leguminosae: Papilionoideae) inferred from molecular phylogenetic analyses of chloroplast and nuclear DNA sequences

Cicer L. (Leguminosae: Papilionoideae) consists of 42 species of herbaceous or semi-shrubby annuals and perennials distributed throughout the temperate zones of the Northern Hemisphere. The origin and geographical relationships of the genus are poorly understood. We studied the geographical diversification and phylogenetic relationships of Cicer using DNA sequence data sampled from two plastid regions, trnK / matK and trnS - trnG , and two nuclear regions, the internal transcribed spacer (ITS) and external transcribed spacer (ETS) regions of nuclear ribosomal DNA, from 30 species. The results from the phylogenetic analyses of combined nuclear and chloroplast sequence data revealed four well-supported geographical groups: a Middle Eastern group, a West-Central Asian group, an Aegean–Mediterranean group, and an African group. Age estimates for Cicer based on methods that do not assume a molecular clock (for example, penalized likelihood) demonstrate that the genus has a Mediterranean origin with considerable diversification in the Miocene/Pliocene epochs. Geological events, such as mountain orogenesis and environmental changes, are major factors for the dispersal of Cicer species. The early divergence of African species and their geographically distinct region in the genus suggest a broader distribution pattern of the genus in the past than at present.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society, 2007, 154 , 175–186.     

On the monophyly of Dactylorhiza Necker ex Nevski (Orchidaceae): is Coeloglossum viride (L.) Hartman a Dactylorhiza?

Previous phylogenetic analyses of Orchidaceae subtribe Orchidinae resulted in the proposal to classify Coeloglossum viride (L.) Hartman within the genus Dactylorhiza in order to maintain its monophyly. In this paper, we report some results that contradict previous studies regarding the monophyly of the traditional Dactylorhiza and its phylogenetic relationship with Coeloglossum. Our results, which combine sequences of the internal and external transcribed spacers of the nuclear ribosomal DNA, support the monophyly of Dactylorhiza , with Coeloglossum being a sister clade. The position of C. viride in the phylogenetic tree, and the considerable morphological differences with respect to Dactylorhiza , incline us to retain both lineages as distinct genera.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 261–269.     

Origin and relationships of the myco-heterotrophic liverwort Cryptothallus mirabilis Malmb. (Metzgeriales, Marchantiophyta)

Heterotrophic life histories have evolved independently numerous times in the angiosperms. In non-vascular embryophytes, heterotrophy is known only in the genus Cryptothallus . Cryptothallus mirabilis obtains photosynthates indirectly from a host tree via a basidiomycete that is simultaneously ectomycorrhizal on the host, a strategy known as myco-heterotrophism. This simple thalloid liverwort was initially described as an albino variant of Aneura pinguis , and the literature varies on whether it should be considered as such, as a distinct species of Aneura , or as a separate genus. Here, the relationships of C. mirabilis within the family Aneuraceae are reconstructed using DNA sequence data from the chloroplast ( rps 4, rps 14, atp B- rbc L spacer, trn G), mitochondrial ( trn S), and nuclear (26S and ITS) genomes. Several allopatric populations of C. mirabilis and of both sympatric species of Aneura (i.e. A. pinguis and A. maxima ) were included. Cryptothallus mirabilis is resolved as having a single origin from within Aneura , and hence the myco-heterotrophic liverwort should be considered as a distinct species of Aneura , rather than an autonomous genus. The fungal symbiont of the photosynthetic A. pinguis is of the same genus, Tulasnella , as that of C. mirabilis , suggesting that the heterotrophic life strategy might have evolved from a pre-existing symbiosis.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 1–12.     

Systematics of the tribe Podalyrieae (Fabaceae) based on DNA, morphological and chemical data

Phylogenetic relationships among nine genera and 28 species of the southern African tribe Podalyrieae were estimated from sequences of the internal transcribed spacer (ITS) of nuclear ribosomal DNA as well as morphological and chemical data. Morphological and ITS sequence data produced cladograms with similar topologies, both supporting the monophyly of Podalyrieae (excluding Hypocalyptus ). The combined data sets indicate that subtribe Xiphothecinae are monophyletic, but embedded within Podalyriinae. The high degree of congruence between previous taxonomic hypotheses and those based on DNA data provides further evidence for the utility of ITS sequences in studying phylogeny.  © 2002 The Linnean Society of London , Botanical Journal of the Linnean Society , 2002, 139 , 159–170.     

A global molecular phylogeny of the fern genus Trichomanes (Hymenophyllaceae) with special reference to stem anatomy

To establish a basis for future taxonomic revisions and to infer the evolutionary traits of Trichomanes s.l. , one of two large filmy fern genera, molecular phylogenetic analyses were conducted using chloroplast rbcL sequences. Sampling covered most of the global distribution range of this genus throughout the tropical and temperate zones, as well as all taxonomically significant species by the addition of 51 samples principally from Asia. The evolution of eight selected characters, which were adopted as taxonomic keys and/or putatively reflect morphological regression, was optimized on the retrieved most parsimonious rbcL trees, together with new observations on the stem anatomy of 45 species. The eight robust clades retrieved within Trichomanes in the rbcL phylogeny conflict with the existing classifications. Our results also suggest that the cup-shaped sorus, the primary diagnostic character of the genus, appears in parallel in the Hymenophyllum lineage, as demonstrated by Pleuromanes (typified by Trichomanes pallidum ) included in the lineage. The suggestion that the regressive character states are homoplastic apomorphies in the evolution of the frond size, stem thickness, root system, and stem anatomy (stele and cortex) probably illustrates a strong tendency towards adaptive evolutionary transition in Trichomanes . © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 155 , 1–27.     

New chromosome counts in the genus Cousinia (Asteraceae) from Iran

Chromosome counts are reported of 38 populations representing 24 species of the genus Cousinia from Iran, one of the main centres of speciation of the genus. Sixteen of the counts are new to science. Our results confirm that Cousinia exhibits a complex dysploid series ranging from x  = 13 to x  = 9. One of the basic chromosome numbers, x  = 9, is new for the genus and must be confirmed. Some considerations on the correlation between chromosome numbers and section classification are made.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 411–419.     

Phyllanthus section Choretropsis (Euphorbiaceae) in Brazil

Section Choretropsis genus Phyllanthus (Euphorbiaceae) is formed by plants whose branches are modified into phylloclades. Despite the suitable characteristics of phylloclades within the Phyllanthus genus, the systematics of these species are poorly understood. Morphological data are presented here to allow future revision of this taxonomic group. The section is represented by nine species distributed in South America, eight of them endemic to Brazil. Our taxonomic studies distinguish the species and propose the synonymization of nine varieties of P. klotzschianus and two varieties of P. flagelliformis based on vegetative and reproductive characters. The diversity of branching and the morphology of phylloclades are discussed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 150 , 131–164.     

Relationships in Patagonian species of Berberis (Berberidaceae) based on the characterization of rDNA internal transcribed spacer sequences

Sequence analysis of the internal transcribed spacer (ITS) of the 18S(ITS1)-5.8S-26S(ITS2) rDNA region was performed in order to analyse the phylogenetic relationships between 13 Patagonian species of the genus Berberis (Berberidaceae). The divergence values between the pairwise sequence in the studied Patagonian species were in the range 2.9–22.9%. The lengths of the ITS1 and ITS2 sequences were in the range 227–231 bp and 220–224 bp, respectively, and the 5.8S sequence was 159 bp throughout all species . B. microphylla sensu Landrum does not appear to be monophyletic based on current sampling. Indeed, we suggest that B. microphylla should be distinguished from B. buxifolia , B. parodii , and B. heterophylla . ITS sequences, together with data obtained from morphological, biochemical, amplified fragment length polymorphism, and cytological characterizations, support the existence of diploid and polyploid hybrid speciation in the genus.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 153 , 321–328.     

High photobiont diversity associated with the euryoecious lichen-forming ascomycete Lecanora rupicola (Lecanoraceae, Ascomycota)

The diversity and phylogenetic position of photobionts in the widespread saxicolous, crustose lichen-forming ascomycete Lecanora rupicola s.l. is presented. The algal partners of this lichen species complex belong to diverse and unrelated lineages in the genus Trebouxia . Specimens were sampled from different habitats and geographical origins. Either whole thallus DNA extractions or minute fragments of the algal layer of the lichen thallus were subjected to polymerase chain reaction, using primers that specifically amplify internal transcribed spacer rDNA of the photobionts. No correlations between different chemical races of L. rupicola with particular lineages of Trebouxia spp. were found. Irrespective of the different algal partners, all lichen thalli abundantly developed ascomata. L. rupicola apparently maintains full fecundity with a low degree of selectivity for photobionts, which promotes the occurrence of this lichen-forming species in ample ecological situations.  © 2006 The Linnean Society of London, Biological Journal of the Linnean Society , 2006, 88 , 283–293.     

A new Mantalania species (Rubiaceae) from Madagascar

Mantalania longipedunculata De Block & A.P. Davis, a new species of Rubiaceae (Gardenieae) from Île Sainte Marie, Madagascar, is described, illustrated, and compared with the three other species in the genus. An extinction risk assessment is given, using the categories and criteria of the World Conservation Union (IUCN).  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 421–424.     

A revision of Cerdia (Caryophyllaceae)

Cerdia is a poorly understood genus of minute cushiony plants endemic to Mexico that is traditionally placed in subfamily Paronychioideae, tribe Polycarpeae (Caryophyllaceae). Morphological observations and phylogenetic analysis of ITS DNA sequences were carried out to determine the number of species, heretofore controversial, that constitute the genus as well as its position within Caryophyllaceae. Samples of Cerdia were collected through its entire range of distribution and together with previous specimens were used in morphological analyses. Nineteen terminal taxa were considered in a phylogenetic analysis with representatives of the different lineages in Caryophyllaceae. Results indicated that Cerdia is a monotypic genus, including only one variable species, C .  virescens , but its phylogenetic affinities remain doubtful.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 1–13.     

Phylogenetic analysis of Nymphaeales using fast-evolving and noncoding chloroplast markers

The Nymphaeales (water-lilies and relatives) represent one of the earliest branching lineages of angiosperms and comprise about 70 aquatic species. Here, we present a comprehensive study of phylogenetic relationships within the Nymphaeales from a dataset containing 24 representatives of the order, including all currently recognized genera and all subgenera of the genus Nymphaea , plus 5 outgroup taxa. Nine different regions of the chloroplast genome − comprising spacers, group II introns, a group I intron, and a protein coding gene − were analysed. This resulted in a character matrix of 6597 positions and an additional 369 characters obtained from coded length mutations. Maximum parsimony and Bayesian analyses of the complete dataset yielded congruent, fully resolved and well-supported trees. Our data confirm the monophyly of the Cabombaceae but do not provide convincing support for the monophyly of Nymphaeaceae with respect to Nuphar . Moreover, the genus Nymphaea is inferred to be paraphyletic with respect to Ondinea , Victoria and Euryale . In fact, the Australian endemic Ondinea forms a highly supported clade with members of the Australian Nymphaea subgenus Anecphya . In addition, Victoria and Euryale are inferred to be closely related to a clade comprising all night-blooming water-lilies ( Nymphaea subgenera Hydrocallis and Lotos ). An experimental approach showed taxon sampling to be of influence on the nodes reconstructed in core Nymphaeaceae. The results underscore that more diverse genera, if not clearly known to be monophyletic, should be represented by all major lineages.  © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 141–163.     

Molecular evidence for phylogenetic relationships of Jacquemontia reclinata House (Convolvulaceae) – a critically endangered species from south Florida

Jacquemontia reclinata House (Convolvulaceae) is a federally listed endangered species endemic to coastal strand habitat of south-eastern Florida. In order to identify the closest relatives of J. reclinata , a phylogenetic reconstruction was performed based on nucleotide sequence data from the internal transcribed spacer region of nuclear ribosomal DNA and from the trnH-psbA intergenic spacer of chloroplast DNA. The three putative relatives of J. reclinata and the majority of Jacquemontia Choicy species known to occur in the Caribbean Islands were included. The strict consensus tree concurs with previous morphological studies, indicating that J. reclinata is closely related to the Caribbean species J. cayensis Britton, J. curtisii Hallier f., and J. havanensis (Jacq.) Urb. These three species and J. reclinata form an unresolved clade. Nucleotide divergence within this clade is low, suggesting that the group is recent, perhaps diversifying after the latest glacial period. These taxa need to be studied further using population-level DNA markers. Most species endemic to the Caribbean Basin form a strongly supported clade. Our phylogeny supports Convolvulus nodiflorus Desr. as part of Jacquemontia . In addition, J. ovalifolia (West) Hallier f. ssp. sandwicensis (A. Gray) K.R. Robertson is sister to the Antillean endemic J. solanifolia (L.) Hallier f. © 2007 The Linnean Society of London, Botanical Journal of the Linnean Society , 2007, 154 , 443–454.     

Molecular variation and speciation in Antitrichia curtipendula s.l. (Leucodontaceae, Bryophyta)

Molecular variation in Antitrichia curtipendula (Hedw.) Brid. s.l. was studied based on the nuclear internal transcribed spacer (ITS) and the chloroplast markers trn L- trn F and rpl 16, and analysed by neighbour joining (for ITS; recombination present), maximum parsimony (chloroplast markers) and TCS (haplotype network). Old World plus E North American populations belong to a different lineage than those of W North America. These are molecularly well differentiated and are treated as A. curtipendula and A. gigantea (Sull. & Lesq.) Kindb. Two distinct groups of Old World haplotypes are separated by one 'missing' haplotype and are interpreted as cryptic species. Tropical African populations share one ITS deletion and form a lineage within one of the cryptic species. Molecular variation within A. gigantea , within each of the two cryptic Old World plus E North American (except tropical African) haplotype groups, and among tropical African populations are of similar magnitude, suggesting that analogous mechanisms and similar time spans explain the found variation. Events related to Pleistocene climatic oscillations are suggested as having caused this differentiation within each group, whereas the African lineage was probably split off before this. Identical tRNA-Gly sequences were found in 33 specimens; new primers were designed for rpl 16 and ITS 1+2.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 341–354.     

Morphological and molecular evidence of natural hybridization between two distantly related Rhododendron species from the Sino-Himalaya

Rhododendron (Ericaceae) is a large woody genus in which hybridization may play an important role in evolution and speciation, particularly in the Sino-Himalayan region, where many interfertile species often occur sympatrically. Natural hybridization between Rhododendron delavayi Franch. (=  R. arboreum ssp. delavayi ) and Rhododendron decorum Franch., which belong to different subsections of subgenus Hymenanthes, was investigated. Material of R. delavayi and R. decorum and their putative hybrids was collected from the wild. On the basis of morphology, chloroplast DNA, nuclear ribosomal DNA, and AFLP profiles, hybrids and parental species were identified. Hybridization occurred in both directions, but was asymmetrical, with R. delavayi as the major maternal parent in the hybrid zone. Most of the hybrids possessed intermediate phenotypes, and amongst the 15 hybrids detected were six F1s, two F2s, one first-generation backcross to R. delavayi , and two first-generation backcrosses to R. decorum . This indicates that, if Rhododendron underwent rapid radiation in this region, it did so in spite of permeable species barriers.  © 2008 The Linnean Society of London, Botanical Journal of the Linnean Society , 2008, 156 , 119–129.     

Systematics and biogeography of Klasea (Asteraceae–Cardueae) and a synopsis of the genus

Klasea , traditionally treated as a section in Serratula , is now widely accepted at the generic level. A classification of the genus is presented here, accommodating the 46 species in ten sections based on nuclear ribosomal DNA external and internal transcribed spacer sequence data and morphology. New combinations for five species and ten subspecies are published, and a new hybrid species is described. The genus ranges from the Iberian Peninsula and north Africa through southern and eastern Europe, west and central Asia to the Himalayas, and the Far East of Russia and China. The ancestral area is in west Asia, most probably eastern Anatolia and northern and western Iran. In this region, representatives of all sections are present. The largest section Klasea diversified most likely in the mountains of central Asia. A key to all Klasea species is provided.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 152 , 435–464.