Molecular phylogenetics,character evolution and systematics of the genus Micranthes (Saxifragaceae)

With c. 85 species, the genus Micranthes is among the larger genera of the Saxifragaceae. It is only distantly related to the morphologically similar genus Saxifraga, in which it has frequently been included as Saxifraga section Micranthes. To study the molecular evolution of Micranthes, we analysed nuclear ribosomal (internal transcribed spacer, ITS) and plastid (trnL–trnF) DNA sequences in a comprehensive set of taxa comprising c. 75% of the species. The molecular phylogenetic tree from the combined dataset revealed eight well‐supported clades of Micranthes. These clades agree in part with previously acknowledged subsections or series of Saxifraga section Micranthes. As these eight groups can also be delineated morphologically, we suggest that they should be recognized as sections of Micranthes. New relationships were also detected for some species and species groups, e.g. section Davuricae sister to sections Intermediae and Merkianae, and M. micranthidifolia as a member of section Micranthes. Species proposed to be excluded from the genus Micranthes for morphological reasons were resolved in the molecular tree in Saxifraga. Many morphological characters surveyed were homoplasious to varying extents. Micromorphological characters support comparatively well the clades in the phylogenetic tree. An updated nomenclature and a taxonomic conspectus of sections and species of Micranthes are provided. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015, 178 , 47–66.     

Evolution and biogeography of the austral genus Phyllocladus (Podocarpaceae)

Aim To infer evolutionary relationships within the genus Phyllocladus and among its close relatives by phylogenetic analysis of DNA sequences. Interpret the inferred relationships in association with the fossil record to examine the origin and diversification of the genus. Location Australasia. Methods Phylogenetic analyses of rbcL, matK and internal transcribed spacer (ITS) sequences representing all of the extant species of Phyllocladus and a selection of outgroups from Podocarpaceae and Araucariaceae. Results The rbcL and matK sequences exhibit little variation within Phyllocladus, but ally its members to Podocarpaceae although its immediate sister remains unclear. The ITS sequences resolve all five species of Phyllocladus and two intraspecific ecotypes of P. alpinus. Main conclusions Phyllocladus forms a distinct lineage that diverged early in the evolutionary history of Podocarpaceae. The fossil record indicates that the genus was more widely distributed and morphologically diverse during the early Tertiary than at present. Although of Mesozoic origin, the level of sequence variation within Phyllocladus suggests that the extant species radiated during the late Tertiary c. 6.3 ± 0.9 Ma. New Zealand is the present centre of species diversity.     

Genome size and chromosome number in the New Zealand species of Schoenus (Cyperaceae)

Schoenus (Cyperaceae) has holocentric chromosomes. Chromosome numbers were counted and nuclear DNA amounts were measured for all the New Zealand species of the genus. Chromosome numbers ranged from 2n = 8 to c. 2n = 90. Two chromosome races, with 2n = 28 and 2n = 56, were found in S. pauciflorus. Flow cytometry using propidium iodide‐stained nuclei was used to measure genome size. A 14.8‐fold variation in 2C DNA content was found, with values ranging from 1.33 to 19.71 pg/2C nucleus. Phylogenetic trees based on sequence variation in the internal transcribed spacer (ITS) region of the 45S ribosomal DNA locus were constructed using several phylogenetic models to reveal possible evolutionary relationships among the New Zealand Schoenus spp. and a sample of Australian Schoenus spp. Analysis revealed heterogeneity of chromosome number, size and DNA C value within clades. Meiosis in four species showed only bivalent formation at metaphase I. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 555–564.     

Complex evolutionary relationships in Origanum section Majorana (Lamiaceae)

Origanum (Lamiaceae) comprises a number of essential oil‐rich species that have been used by humans for centuries. Today, the four species of section Majorana (O. onites, O. dubium, O. majorana and O. syriacum) are amongst the most widely used. Despite the importance of this section, phylogenetic relationships and species boundaries amongst its four taxa are unclear. In the present investigation, we used DNA sequence data from two nuclear regions [internal transcribed spacer (ITS) and 1‐deoxy‐d ‐xylulose 5‐phosphate synthase (DXS)] as well as five microsatellite loci to test the taxonomic status of the four species of section Majorana. The combined DNA data revealed O. onites and O. syriacum as the older species in the section. Origanum majorana descends directly from O. syriacum. Origanum dubium was found to be of hybridogenous origin showing attributes of O. onites, O. syriacum and a third, unknown, Origanum species. Both sequence and microsatellite analyses provided evidence for recent hybridization between O. onites and O. dubium in Turkey. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013 , 171 , 667–686.     

MONOPHYLY OF ANEUPLOID ASTRAGALUS (FABACEAE): EVIDENCE FROM NUCLEAR RIBOSOMAL DNA INTERNAL TRANSCRIBED SPACER SEQUENCES

Evolutionary relationships within Astragalus L. (Fabaceae) were inferred from nucleotide sequence variation in nuclear ribosomal DNA of both New World and Old World species. The internal transcribed spacer regions (ITS) of 18S–26S nuclear ribosomal DNA from representatives of 26 species of Astragalus, three species of Oxytropis DC., and two outgroup taxa were analyzed by polymerase chain reaction amplification and direct DNA sequencing. The length of the ITS 1 region within these taxa varied from 221 to 231 bp, while ITS 2 varied in length from 207 to 217 bp. Of the aligned, unambiguous positions, approximately 34% were variable in each spacer region. In pairwise comparisons among Astragalus species and outgroup taxa, sequence divergence at these sites ranged from 0 to 18.8% in ITS 1 and from 0 to 21.7% in ITS 2. Parsimony analyses of these sequences resulted in a well-resolved phylogeny that is highly concordant with previous cytogenetic and chloroplast DNA evidence for a major phylogenetic division in the genus. These data suggest that the New World aneuploid species of Astragalus form a monophyletic but morphologically cryptic group derived from euploid species of Old World (Eurasian) origin, which are consequently paraphyletic.     

Chromosome counts and genome size of Leontopodium species (Asteraceae: Gnaphalieae) from south‐western China

Chromosome counts and genome sizes are reported from six species of Leontopodium: five from the centre of diversity in south‐western China, and L. japonicum from cultivation. Previously published chromosome counts for the genus are also compiled. Genome size (1C) in diploids ranges from 0.93 pg (L. dedeckensii) to 1.14 pg (L. cf. stracheyi) and 1.93 pg for tetraploid L. sinense. Leontopodium artemisiifolium had one pair of heteromorphic chromosomes. Leontopodium japonicum accessions showed variation in ploidy levels. Polyploidy, including autopolyploidy, is frequent in the genus. Variation is seen in basic chromosome number, including between species in the centre of diversity of the genus, where x = 12 or 13, but also within species among previously published counts. This variation does not correspond to currently inferred infrageneric groupings, and indicates both the importance of large‐scale chromosome evolution and the need for more in‐depth taxonomic work in a genus that shows little DNA sequence variation. © 2013 The Linnean Society of London     

Amphitropic amphiantarctic disjunctions in Apiaceae subfamily Apioideae

Aim Four genera of the plant family Apiaceae subfamily Apioideae –Apium, Chaerophyllum, Daucus and Lilaeopsis– are characterized by amphitropic and amphiantarctic distribution patterns, and in Australasia the subfamily is also represented by the tribe Aciphylleae. We infer the molecular ages of achieving amphitropic distribution for these lineages, reconstruct the biogeographical histories of Apium, Chaerophyllum, Daucus and Lilaeopsis, and identify the sister group of Aciphylleae. Location Worldwide, with an emphasis on South America and Australasia. Methods Divergence times were estimated employing a Bayesian approach (beast ) with fossil pollen of basal apioids as calibration points and using a data set of nuclear ribosomal DNA internal transcribed spacer (nrDNA ITS) sequences from 284 accessions of Apioideae. Additionally, maximum‐likelihood analyses were performed for data subsets comprising Apium, Daucus and Lilaeopsis. For Chaerophyllum, maximum‐likelihood and beast analyses were carried out using combined chloroplast DNA and ITS data. Biogeographical scenarios were inferred using diva and lagrange . Results The sister group to Aciphylleae is the Sino‐Himalayan Acronema clade and the divergence between these two lineages is dated at 34.8 Ma, whereas the radiation of Aciphylleae started 11.0 Ma. A Northern Hemispheric origin was inferred for Apium, Chaerophyllum and Daucus, whereas Lilaeopsis probably originated in South America following a dispersal of its ancestor from North America. Chaerophyllum, Daucus and Lilaeopsis dispersed to the Southern Hemisphere at 5.3, 7.0 and 27.9 Ma, respectively. For Apium, two dispersals from Europe were inferred: to South America at 6.3 Ma, and to southern Africa at 3.9 Ma. The taxa migrated along the land masses of North and South America (Daucus, Lilaeopsis) and Africa (Apium) or by direct transoceanic dispersals through the Atlantic (Apium) or the Pacific (Chaerophyllum). Within the Southern Hemisphere they dispersed both westwards (Apium, Daucus, Lilaeopsis) and eastwards (Chaerophyllum, Lilaeopsis). For Chaerophyllum and Lilaeopsis, subsequent dispersal events to the Northern Hemisphere were also inferred. Main conclusions Similar timing, contrasted with the diversity of migration routes, suggests that the dispersal events of these umbellifer taxa (and many other amphitropic amphiantarctic genera) were facilitated by favourable ecological conditions in the Southern Hemisphere (climatic cooling of the late Palaeogene/early Neogene) rather than by increased dispersal opportunities.     

Molecular phylogenetic analysis of Tulipa (Liliaceae) based on noncoding plastid and nuclear DNA sequences with an emphasis on Turkey

We investigated the phylogenetic relationships in Tulipa in Turkey using DNA sequences from the plastid trnL‐trnF region and the internal transcribed spacer (ITS) of nuclear ribosomal DNA. We generated trnL‐trnF and nuclear ITS sequences for 11 Tulipa spp. from Turkey and compared the utility of trnL‐trnF and ITS sequences for phylogenetic analysis. Neighbor‐joining, Bayesian and maximum parsimony methods were implemented using the same matrices. Our study of Tulipa based on molecular data revealed congruent results with previous studies. Despite the relatively lower resolution of trnL‐trnF than that of ITS, both sequence matrices generated similar results. Three clades were clearly distinguished, corresponding to subgenera Tulipa, Eriostemones and Orithyia. It is not fully resolved whether Clusianae should be recognized as a separate section of subgenus Tulipa or a distinct subgenus. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 270–279.     

Parallel evolution of flower reduction in two alpine Soldanella species (Primulaceae)

The European endemic Soldanella has traditionally been divided into two morphologically well‐defined sections. Section Tubiflores contains two species growing in high‐elevation habitats, whereas most of the 14 species of section Soldanella inhabit montane forests. Section Tubiflores has a reduced floral morphology compared with section Soldanella. A previous phylogenetic study based on internal transcribed spacer (ITS) and AFLP data has revealed that, although the genus Soldanella itself is monophyletic, both sections are paraphyletic. Soldanella alpina (section Soldanella) forms a clade with S. minima and S. pusilla (section Tubiflores), and the grouping of S. alpina with S. pusilla has been hypothesized to be the result of hybridization between S. pusilla and an unidentified species of section Soldanella. We re‐examined the phylogenetic relationships among the above species using additional sequence data (plastid DNA) and increasing the sample for ITS and AFLP data. Our new data confirmed that S. alpina is most closely related to S. pusilla. However, our data do not provide any evidence in support of the hypothesis that S. alpina is a hybrid species. In consequence, we consider it likely that the two species of section Tubiflores originated independently. The reduced floral morphology of these two alpine species is probably evidence for increased levels of self‐pollination, ensuring reproductive success in a high‐altitude habitat. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 175 , 409–422.     

Teleomorph-anamorph relationships and reclassification of <Emphasis Type="Italic">Cordyceps cuboidea</Emphasis> and its allied species

Based on morphological characteristics and molecular phylogeny, we reclassified Cordyceps cuboidea and allied species C. alboperitheciata, C. prolifica, and Ophiocordyceps ryogamiensis. We investigated their teleomorph-anamorph relationships and revealed that these four species have Hirsutella-like anamorphs with morphological differences between them. By analyzing their molecular phylogeny, inferred from DNA sequences of internal transcribed spacer (ITS) and large subunit (LSU) D1/D2 region of rDNA, they were separated into four close-knit clades. Although C. prolifica and O. ryogamiensis formed their own clades, isolates of C. cuboidea separated into two clades, i.e., a true C. cuboidea clade and one resembling a new species, the O. paracuboidea clade. The latter two species are distinguished by the fruiting region of the stroma. In addition, C. alboperitheciata is regarded as a synonym of C. cuboidea. From the morphology, teleomorph-anamorph relationships, and molecular phylogeny, we concluded these species should be assigned to the genus Ophiocordyceps.     

Phylogeny of Bonatea (Orchidaceae: Habenariinae) based on molecular and morphological data

The genus Bonatea is widely distributed throughout southern and eastern Africa. Considerable debate surrounds the generic status of Bonatea, but there have been neither previous studies of evolutionary relationships among Bonatea species, nor any tests of the monophyly of the genus in relation to its close relative Habenaria. We investigated phylogenetic relationships between Bonatea and selected Habenaria species using morphology, as well as sequences of the chloroplast gene matK and the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA. A fully resolved cladogram was obtained using morphological data, but neither the ITS, matK, nor combined data sets yielded well-resolved and well-supported phylogenetic structure for Bonatea. There is poor congruence between ITS and matK data for interspecific relationships in Bonatea, whilst the morphological results are largely congruent with the ITS analysis. Relative to Habenaria, there is little sequence variation between Bonatea species, which could indicate a recent and rapid radiation of Bonatea. Although the sampled Bonatea species form a distinct clade, more extensive sampling of Habenaria would be required to establish unambiguously whether or not Bonatea is monophyletic.     

Molecular phylogeny,diagnostics, and diversity of plant‐parasitic nematodes of the genus Hemicycliophora (Nematoda: Hemicycliophoridae)

The genus Hemicycliophora (Nematoda: Hemicycliophoridae) contains 132 valid species of plant‐parasitic nematodes, collectively known as ‘sheath nematodes’. Hemicycliophora spp. are characterized morphologically by a long stylet with rounded basal knobs and a cuticular sheath, present in juvenile and adult stages. Populations of 20 valid and 14 putative species of Hemicycliophora and Loofia from several countries were characterized morphologically using light (LM) and scanning electron microscopy (SEM) and molecularly using the D2‐D3 segments of 28S rRNA and internal transcribed spacer (ITS) rRNA gene sequences. LM and SEM observations provided new details on the morphology of these species. PCR‐restriction fragment length polymorphisms (PCR‐RFLPs) of the D2‐D3 of 28S rDNA were proposed for identification of the species. Phylogenetic relationships within populations of 36 species of the genus Hemicycliophora using 102 D2‐D3 of 28S rDNA and 97 ITS rRNA gene sequences as inferred from Bayesian analysis are reconstructed and discussed. Ancestral state reconstructions of diagnostic characters (body and stylet length, number of body annuli, shape of vulval lip and tail), using maximum parsimony and Bayesian inference, revealed that none of the traits are individually reliable characters for classifying the studied sheath nematode. The Shimodaira–Hasegawa test rejected the validity of the genus Loofia. This is the most complete phylogenetic analysis of Hemicycliophora species conducted so far. © 2014 The Linnean Society of London     

Molecular phylogeny of genus Vigna subgenus Ceratotropis based on rDNA ITS and atpB-rbcL intergenic spacer of cpDNA sequences

The genetic diversity and phylogenetic relationships among species in the genus Vigna subgenus Ceratotropis were investigated using sequence data from the ribosomal DNA ITS and atpB-rbcL intergenic spacer of chloroplast DNA regions. While both sets of sequences were of similar lengths about 700bp the rDNA-ITS was more informative than atpB-rbcL having 170% more polymorphic sites and five times as many parsimony-informative sites. The atpB-rbcL spacer may be appropriate for analysis of taxa above the species level in the genus Vigna. Results of analyzing rDNA-ITS revealed, with low level of statistical bias, separation of the subgenus into three groups that correspond to the three sections Aconitifoliae, Angulares, and Ceratotropis. The ancestral section is Aconitifoliae based on comparison with the outgroup species cowpea, Vigna unguiculata. The V. minima complex, V. minima, V. riukiuensis, and V. nakashimae, has a distinct evolutionary path within section Angulares. Other species in section Angulares are very closely related except V. trinervia. Vigna trinervia has an intermediate position between sections. Sequence data suggests one genome donor to V. reflexo-pilosa came from a lineage within section Angulares close to V. exilis, V. hirtella, and V. umbellata. Data presented supports the view that section Angulares is the most recently diversified section in the subgenus, as inferred by short terminal branch lengths among the species of this section.     

Phylogenetic analysis of eastern Asian and eastern North American disjunct Lespedeza (Fabaceae) inferred from nuclear ribosomal ITS and plastid region sequences

Lespedeza (tribe Desmodieae, Fabaceae) follows a disjunct distribution in eastern Asia and eastern North America. Phylogenetic relationships among its species and related taxa were inferred from nuclear ribosomal internal transcribed spacer (ITS) and plastid sequences (trnH‐psbA, psbK‐psbI, trnK‐matK and rpoC1). We examined 35 species of Lespedeza, two of Kummerowia and one of Campylotropis, the sole constituents of the Lespedeza group. An analysis of these data revealed that the genus Campylotropis is sister to the other two genera. However, we were unable to resolve the relationships between Kummerowia and Lespedeza in the strict consensus trees of parsimony analyses based on plastid and combined DNA data. In the genus Lespedeza, the Old World subgenus Macrolespedeza is monophyletic, whereas the transcontinental subgenus Lespedeza is paraphyletic. Monophyly of eastern Asian species and of North American species is strongly supported. Although inconsistent with the traditional classification, this phylogenetic finding is consistent with seedling morphology. Three subgroups recognized in subgenus Macrolespedeza were unresolved in our phylogenetic trees. An incongruence length difference (ILD) test indicated that the two partitions (nuclear ITS and plastid sequences) were significantly incongruent, perhaps because of hybridization between species in Lespedeza. Most of the primary clades of tribe Desmodieae are Asian, implying that the relatively few New World ones, such as those in Lespedeza, are more recently derived from Asia. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 221–235.     

Fewer species of Argosarchus and Clitarchus stick insects (Phasmida, Phasmatinae): evidence from nuclear and mitochondrial DNA sequence data

The systematics of three genera of New Zealand stick insect in the subfamily Phasmatinae were investigated in light of inconsistencies in morphological variability within and among species. We sequenced a region of the mitochondrial genome, cytochrome oxidase (COI & COII; 1448 bp), and a nuclear marker, the internal transcribed spacers (ITS1 & ITS2; 1804 bp) from 49 stick insects. Mitochondrial DNA sequence divergences among the three genera (Argosarchus, Clitarchus and Acanthoxyla) were relatively high (～12%) but the current taxonomy within genera was not supported. Within the three genera, low levels of genetic divergence were observed at both nuclear and mitochondrial loci, and phylogenetic analyses failed to support reciprocal monophyly of the two species in Argosarchus and Clitarchus. Sympatric individuals of Argosarchus spiniger and A. horridus were more closely related to each other than to members of their respective morphospecies from elsewhere. No males were found in the Chatham Island population of Argosarchus and although this population has been referred to as A. schauinslandi, genetic and morphological evidence does not support its distinction from mainland Argosarchus. Likewise, individuals identified as Clitarchus tuberculatus were genetically identical, or most similar to, C. hookeri from the same or adjacent sites rather then grouping with the stick insects they were morphologically most similar to. Lack of spatial, behavioural or ecological evidence concordant with the described species A. spiniger, A. schauinslandi and C. tuberculatus leads us to infer that these species are synonymies of A. horridus and C. hookeri respectively. We conclude that Argosarchus and Clitarchus have each been over‐split and actually consist of a single morphologically polymorphic, facultative parthenogenetic species. The genus Acanthoxyla with eight described species also has low levels of genetic divergence, similar to those found in Argosarchus and Clitarchus. A possible hybrid origin of Acanthoxyla involving its sister genus Clitarchus is implied by sharing of ITS sequence variants, but further sampling is needed before the species status of these obligate parthenogenetic lineages can be resolved. In contrast to some New Zealand Orthoptera, the Phasmatinae show little genetic variation suggesting coalescence in recent times, possibly reflecting lineage sorting in the Pleistocene.     

Biogeographical,ecological and morphological structure in a phylogenetic analysis of Ateleia (Swartzieae,Fabaceae) derived from combined molecular,morphological and chemical data

A phylogenetic analysis of combined morphological, chemical and ITS/5.8S sequence data reveals that species of Ateleia are often more genetically than morphologically divergent, and that species thought to be most closely related morphologically are distant relatives within the genus. Ateleia shows niche conservatism, with most species confined to seasonally dry tropical forest in Central America and the Caribbean, and fewer species in the same biome in South America. Four independent transitions to wet forests may have occurred in the genus. The estimated ages of Ateleia lineages spanning Central and South America are either older or younger than the estimated age of closure of the Isthmus of Panama. The older dates clearly suggest that over‐water dispersal is responsible for the distribution of Ateleia that includes the Caribbean Islands. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 39–53.     

A new meristematic fungus,Pseudotaeniolina globosa

A new species of Pseudotaeniolina, a genus of anamorphic, melanized fungi with meristematic development, is described. The species is compared to morphologically similar taxa among which are Trimmatostroma and Coniosporium. Its novelty is supported by SSU (small subunit) and ITS (internal transcribed spacer) rDNA sequence data. This revised version was published online in June 2006 with corrections to the Cover Date.     

Resurrection in Carapa (Meliaceae): a reassessment of morphological variation and species boundaries using multivariate methods in a phylogenetic context

The taxonomy of the amphi‐Atlantic tree genus Carapa (Meliaceae) has long been controversial. Of the three species currently recognized in the genus, two are known to present substantial morphological variation that has been used in the past to distinguish several taxa, most of which are currently placed in synonymy. Here, a combination of field observations, univariate analyses of leaf, floral and seed characters and principal coordinate analyses of floral characters in the context of a molecular phylogenetic analysis was used to investigate the patterns of variation and delimit morphological species anew in the genus. These results support the recognition of 27 species in Carapa, of which 16 are previously described and 11 are new. In general, phylogenetically related species occurred in the same geographical area, but were morphologically distinct. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 165 , 186–221.     

Evolution of St Helena arborescent Astereae (Asteraceae): relationships of the genera Commidendrum and Melanodendron

The cladistic relationships of endemic Commidendrum (four species) and Melanodendron (one species) from St Helena were inferred from sequences of ITS1 and ITS2 of nuclear ribosomal DNA. Despite showing a range of morphological and ecological variation, the four species of Commidendrum , C. spurium , C. robustum , C. rotundifolium , and C. rugosum , form a closely related monophyletic group with percentage sequence divergence between 0.2 and 0.9%. Melanodendron integrifolium is sister to Commidendrum indicating that the two genera may have evolved from a common ancestor that arrived in St Helena via a single dispersal event. The closest relatives of Commidendrum and Melanodendron appear to be South African, in the predominantly shrubby genus Felicia , although further sampling of South African Astereae is required. We discuss the evolution and adaptive radiation of these rare and threatened species with particular reference to the possible role of heterochrony.  © 2004 The Linnean Society of London, Botanical Journal of the Linnean Society , 2004, 144 , 69–83.