Resolving the unresolved tribe: a molecular phylogenetic framework for the Merremieae (Convolvulaceae)

Tribe Merremieae, as currently circumscribed, comprise c. 120 species classified in seven genera, the largest of which (Merremia) is morphologically heterogeneous. Previous studies, with limited sampling, have suggested that neither Merremieae nor Merremia are monophyletic. In the present study, the monophyly of Merremia and its allied genera was re‐assessed, sampling 57 species of Merremieae for the plastid matK, trnL–trnF and rps16 regions and the nuclear internal transcribed spacer (ITS) region. All genera of Merremieae and all major morphotypes in Merremia were represented. Phylogenetic analyses resolve Merremieae in a clade with Ipomoeae, Convolvuleae and Daustinia montana. Merremia is confirmed as polyphyletic and a number of well‐supported and morphologically distinct clades in Merremieae are recognized which accommodate most of the species in the tribe. These provide a framework for a generic revision of the assemblage. © 2015 The Linnean Society of London, Botanical Journal of the Linnean Society, 2015.     

Phylogenetic systematics of Erythronium (Liliaceae): morphological and molecular analyses

For a nearly complete set of species of Erythronium (Liliaceae), we examined two plastid loci (the rps16 intron and the 5′ trnK intron, excluding the matK exon), one nuclear locus (nrITS) and morphology to evaluate species relationships and that of Erythronium to Amana, the putatively most closely allied genus. A matrix of morphological characters was developed through observation of around 900 living and herbarium specimens; evolution of these was examined using character optimization on the combined (total‐evidence) tree. Parsimony methods were used to examine the morphological and molecular data sets produced, both separately and in combination, with Bayesian methods also used on the molecular data sets. These established that the genus is probably sister to Amana (although most analyses placed Amana inside Erythronium) and that Tulipa is sister to the pair of Erythronium and Amana. Within Erythronium, there are three strongly supported geographically distinct clades: (1) Eurasian and (2) eastern and (3) western North American. Separation of species in these three clades is less clear, particularly among the western North American taxa. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, ●●, ●●–●●.     

Molecular phylogenetics of the juno irises,Iris subgenus Scorpiris (Iridaceae), based on six plastid markers

Relationships among the roughly 55 species of Iris subgenus Scorpiris have been studied. A matrix of six plastid DNA regions (matK, rpl14‐rps8 spacer, infA‐rpl36 spacer, trnE‐trnT spacer, trnL intron and trnL‐F spacer) was produced from 57 accessions (52 taxa) and analysed with both parsimony and Bayesian methods. Five major clades are identified, of which four have strong geographical correlations, whereas the fifth corresponds to Iris section Physocaulon. In our results, several species are placed with species not previously considered to be related, although, in some cases, there are morphological characters that suggest that these newly indicated relationships are reasonable. For some of the other oddly grouped species, we can only assume that remarkable parallelisms in morphology have occurred or hybridization is involved. Presently, with plastid DNA as our only comprehensive data resource, we are not able to evaluate more thoroughly these more puzzling associations of species. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167 , 281–300.     

An integrative approach to characterize cryptic species in the Thoracostoma trachygaster Hope, 1967 complex (Nematoda: Leptosomatidae)

Nematode diversity may seriously be underestimated when taking into account cryptic speciation. Thoracostoma trachygaster is commonly found in kelp holdfasts along the California coastline and was recently shown to consist of at least two distinct molecular clades (I and II). Here, we provide detailed morphological analysis of both clades, based on measurements taken from video vouchers of respectively eight and 16 individuals from the previous study, as well as 80 newly collected specimens from four Californian beaches. The latter were vouchered, measured, and then subjected to molecular analyses of the mitochondrial cytochrome oxidase c subunit I (COI) gene, and the ribosomal D2D3 and internal transcribed spacer (ITS) regions. This integrative approach shows that the three molecular clades are phylogenetically and morphologically distinct species, but a combination of morphological characters is needed to distinguish them. Two new species, Thoracostoma fatimae sp. nov. and Thoracostoma igniferum sp. nov. , are identified and described. The spicule length of T. fatimae sp. nov. is significantly shorter than that of T. trachygaster. Thoracostoma igniferum sp. nov. can be distinguished by the irregular posterior edge of the cephalic capsule and the two internal subdorsal tropis‐like projections in the wall of the cephalic capsule, which are lacking in T. fatimae sp. nov. and T. trachygaster. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 164 , 18–35.     

Unravelling the evolutionary history of the polyploid complex Ranunculus parnassiifolius (Ranunculaceae)

Ranunculus L. represents the largest genus within Ranunculaceae, comprising more than 600 species with a worldwide distribution. However, there are still many gaps in our knowledge of the infrageneric taxonomy and evolution of Ranunculus. In this regard, intraspecific variation of the polyploid complex Ranunculus parnassiifolius remains under discussion. To reconstruct the biogeographical history of the polyploid complex R. parnassiifolius, 20 populations distributed throughout the Cantabrian Mountains, Pyrenees, and Alps were investigated. Phylogenetic studies were based on nuclear internal transcribed spacers (ITS) and plastid (rpl32‐trnL, rps16‐trnQ) sequence data, analysed using Bayesian approaches as well as the evolution of morphological characters. Additionally, biogeographical patterns were conducted using statistical dispersal–vicariance analysis. The analyses presented here support the recognition of two evolutionary independent units: R. cabrerensis sensu lato (s.l.) and R. parnassiifolius s.l. Furthermore gradual speciation depending on the biogeographical territory is proposed, and optimal reconstructions have probably favoured the ancestor of Ranunculus parnassiifolius as originating in the Iberian Peninsula. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107 , 477–493.     

Characterization and distribution of <Emphasis Type="Italic">Daucus</Emphasis> species in Syria

Syria is considered as one of the important centres for Daucus diversity including Daucus carota. Therefore, it is essential to study the distribution and characterization of these species in Syria. An exploration of plants belonging to the Apiaceae family was conducted on road and field sides in several areas of Syria. Seeds (fruits) from these plants have been also collected. The seeds were sown in pots containing peatmoss in a glasshouse and emerging plants were grown until flowering and seed formation. The plants were classified based on leaf, umbel, and seed shape. Proteins were extracted from the leaves and analysed using electrophoresis to establish genetic relationships among species. Seven Daucus species have been identified to grow in Syria. These are D. aureus, D. bicolor, D. carota, D. durieua, D. guttatus, D. littoralis, and D. muricatus. Isozyme and total protein analysis, cluster analysis, and correlation matrix have revealed considerable genetic variation among studied Daucus species. Wild carrot (D. carota) came in one group with its cultivated form (D. carota ssp. sativus) and the closest species to them was D. guttatus. Species D. bicolor and D. durieua were in the same group and D. aureus and D. littoralis were in another group farther from the previous groups. The farthest species on the genetic tree was D. muricatus.     

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.     

Phylogenetics and biogeography of Nephrolepis – a tale of old settlers and young tramps

The phylogenetic relationships and biogeographical history of the tropical genus Nephrolepis, a popular ornamental fern, are investigated using plastid DNA data from three regions: rbcL, rps4 plus the rps4‐trnS intergenic spacer (IGS) and the trnG intron plus the trnG‐trnR IGS. Our taxon sampling includes all but one of the 19 species of the genus. We confirm the monophyly of Nephrolepis, resolve infrageneric relationships and propose monophyly of the widespread species Nephrolepis biserrata and Nephrolepis abrupta, awaiting a denser sampling of Nephrolepis cordifolia and Nephrolepis undulata. The controversial inclusion of Nephrolepis in Lomariopsidaceae is not clearly supported. With a view to identifying synapomorphies for the clades retrieved, we reconstruct the evolution in Nephrolepis of sorus position and indusium shape. Finally, based on an estimation of divergence times and reconstruction of ancestral distributions for the genus, we propose an origin of the crown group in the Eocene in the forests of the Laurasian tropical belt, from where two main lineages would have dispersed and become isolated, one in the Neotropics and the other in Asia–Australasia. From this clear biogeographical pattern, some species, probably of Asian–Australasian origin, show recent range expansions, now spanning the Palaeotropics or the pantropical zone. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 164 , 113–127.     

Ultrastructural investigations of mature embryo sacs of Daaucus carota,D. aureus and D. muricatus — possible cytological explanations of paternal plastid inheritance

Summary The embryo sacs of Daucus carota, D. Aureus and D. muricatus are of the Polygonum-type. They contain one egg cell, two synergids, a giant central cell and three antipodal cells that are to a great extent degenerated. The species of Daucus investigated have an egg cell with a vacuole that is large in comparison to the amount of cytoplasm. The most extreme case of reduced cytoplasm with respect to the volume of the vacuole occurs in D. muricatus. The egg cell of this species contains only very few intact plastids and other cytoplasmic organelles. Paternal plastid inheritance in the cross D. muricatus × D. carota is discussed in connection with the small number of cytoplasmic organelles in the female gamete of D. muricatus.     

Molecular phylogeny of the subgenus Holothuria (Selenkothuria) Deichmann, 1958 (Holothuroidea: Aspidochirotida)

The subgenus Selenkothuria comprises 12 species of tropical shallow water sea cucumbers that share morphological features, such as rods in the body wall and tube feet, modified tentacles for suspension feeding, and cryptic colours. The taxonomic status of this taxon has been controversial, but currently it is accepted as a subgenus of the genus Holothuria. Phylogenetic analyses of mitochondrial genes [cytochrome c oxidase subunit 1 (COI), 16S RNA] of ten species of Selenkothuria and related subgenera showed the polyphyly of this subgenus; monophyly was rejected by a likelihood ratio test. A geographical split divides the species of this subgenus into three different groups: one Indo‐West‐Pacific (IWP) group and two American groups. The IWP group is more closely related to Holothuria (Semperothuria) cinerascens and to other subgenera such as Roweothuria, Holothuria, and Vaneyothuria, whereas the two American groups are more closely related to each other and to some species of the subgenus Halodeima. These results suggest multiple parallel originations and diversification of ossicle morphology within the subgenus Selenkothuria. The current scheme of subgenera for the genus Holothuria is not supported, suggesting the need for a new classification. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 109–120.     

Patterns of hybridization in a multispecies hybrid zone in the Ranunculus cantoniensis complex (Ranunculaceae)

Simultaneous hybridizations among three or more parental taxa occur in nature, but these have rarely been analysed. The present study investigates the natural hybridization of diploid members of the Ranunculus cantoniensis complex over a microgeographical area in south‐western China. Sequence information from maternally inherited plastid DNA (trnQ‐rps16 and rpL32‐trnL) and biparentally inherited nuclear ribosomal DNA was used to identify hybrids, and these were further confirmed by a dramatic reduction in pollen viability. The populations from the contact zone contained individuals that had more than two nuclear ribosomal internal transcribed spacer (nrITS) types; in addition, a network analysis revealed the presence of hard conflicts between the nuclear and plastid DNA data. These results prove that R. trigonus and R. silerifolius var. dolicanthus have relatively little reproductive isolation from each other, leading to a high gene flow rate in contact populations. The four investigated species can hybridize with each other in this contact zone, forming seven hybrid types. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 174 , 227–239.     

Variability,genetic structure and phylogeography of the dolomitophilous species Convolvulus boissieri (Convolvulaceae) in the Baetic ranges,inferred from AFLPs,plastid DNA and ITS sequences

Convolvulus boissieri is an edaphic endemic plant which grows in the Baetic ranges always in association with high mountain xeric dolomitic outcrops. As these dolomitic areas appear in a ‘soil‐island’ pattern, the distribution of this species is disjunct. Populations of this species frequently include a low number of individuals, which could have an important impact on their genetic diversity and viability. Convolvulus boissieri provides an excellent opportunity to study the genetic and phylogeographical aspects of species linked to dolomites. We used amplified fragment length polymorphism markers and nuclear (internal transcribed spacer region of the nuclear ribosomal cistron) and plastid sequences (trnL‐trnF, rpl32‐trnL and trnQ‐5′rps16). Data were generated from 15 populations, representing the distribution area of the species. For sequence analysis and estimation of divergence times we also used sequences from other Convolvulus species. Results revealed low intrapopulational genetic diversity and a strong interpopulational structure. Furthermore, we found clear‐cut differentiation caused by the existence of two large population groups separated by the Guadiana Menor river basin. Estimation of divergence times indicated that divergence took place during the Pleistocene glaciations. Genetic diversity and differentiation are similar to those other species exhibiting naturally fragmented distribution with a sky islands pattern. In phylogeographical terms, the successive glaciation–interglaciation cycles caused the species to spread from the western sites to eastern sites, the latter being more exposed to the effects of glaciation. © 2014 The Linnean Society of London, Botanical Journal of the Linnean Society, 2014, 176 , 506–523.     

Reappraisal of Primula ranunculoides (Primulaceae), an endangered species endemic to China,based on morphological,molecular genetic and reproductive characters

The taxonomic status of Primula ranunculoides and other members of section Ranunuculoides is reappraised here based on data from morphological, reproductive and molecular characters. Multivariate analysis of morphological characters indicates that P. ranunculoides is a coherent species that can be distinguished from its sectional congeners P. cicutariifolia and P. merrilliana by the characters of simple kidney‐shaped outer leaves and the unique clonal reproductive ability by which apices of the scape differentiate into bulblets at the late phases of flowering. Recognition of P. ranunculoides at the specific level is also supported by palynological characters, breeding system, cross pollination results and molecular phylogenetic analysis of nrDNA internal transcribed spacer sequences. A taxonomic revision of section Ranunuculoides is presented and a possible mechanism of speciation discussed. © 2012 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 169 , 338–349.     

Phylogenetic relationships in the genus Agathemera (Insecta: Phasmatodea) inferred from the genes 16S,COI and H3

We present a phylogenetic analysis that includes all known species of Agathemera, using as outgroup four species of the genera Heteronemia, Spinonemia, Monticomorpha, and Anisomorpha. Phylogenetic inference was based on three genes, 16S, COI (mitochondrial markers) and H3 (nuclear marker), based on the maximum‐parsimony, maximum‐likelihood and Bayesian inference methods. Our results show that the genus Agathemera is monophyletic; six of its eight species showed phylogenetic support, while the group A. claraziana + A. millepunctata was not resolved. The resulting topology shows two major clades, the first with A. maculafulgens, A. luteola, A. crassa, A. millepunctata, and A. claraziana, and the second including A. grylloidea, A. mesoauriculae, and A. elegans. Species of the first clade have large mesonotal processes and are found mainly east of the Andes, except for A. crassa. Members of the second clade have small or absent mesonotal processes and are distributed mainly to the west of the Andes. © 2012 The Linnean Society of London, Zoological Journal of the Linnean Society, 2012, 165 , 63–72.     

Analysis of genetic variability within the genus Petromyces

Phenotypic and genotypic features of three teleomorphic species, Petromyces alliaceus, P. albertensis and P. muricatus and some related anamorphic Aspergillus species were compared. The dendrogram based on carbon source utilisation data revealed a close relationship between P. muricatus and the A. ochraceus strains examined. P. alliaceus and P. albertensis strains were very closely related to each other. A dendrogram with similar topology was obtained by analysing sequences of the intergenic transcribed spacer regions of representatives of these species. P. alliaceus and P. albertensis strains could only be distinguished by the random amplified polymorphic DNA technique. These strains possibly represent a single species closely related to Aspergillus section Flavi, while the anamorph of P. muricatus is a member of Aspergillus section Circumdati. Our results indicate that Aspergillus section Circumdati is in need of taxonomic revision.     

Drought avoidance and the effect of local topography on trees in the understorey of Bornean lowland rain forest

The water relations of two tree species in the Euphorbiaceae werecompared to test in part a hypothesis that the forest understorey plays anintegral role in drought response. At Danum, Sabah, the relatively commonspecies Dimorphocalyx muricatus is associated with ridgeswhilst another species, Mallotus wrayi, occurs widely bothon ridges and lower slopes. Sets of subplots within two 4 -hapermanent plots in this lowland dipterocarp rain forest, were positioned onridges and lower slopes. Soil water potentials were recorded in1995–1997,and leaf water potentials were measured on six occasions. Soil water potentialson the ridges (–0.047 MPa) were significantly lower than onthe lower slopes (–0.012 MPa), but during the driest periodin May 1997 they fell to similarly low levels on both sites (–0.53MPa). A weighted 40-day accumulated rainfall index was developedtomodel the soil water potentials. At dry times, D.muricatus(ridge) had significantly higher pre-dawn (–0.21 v.–0.57 MPa) and mid-day (–0.59 v.–1.77 MPa) leaf water potentials than M.wrayi (mean of ridge and lower slope). Leaf osmotic potentials ofM. wrayi on the ridges were lower (–1.63MPa) than on lower slopes (–1.09 MPa), withthose for D. muricatus being intermediate (–1.29MPa): both species adjusted osmotically between wet and dry times.D. muricatus trees were more deeply rooted thanM. wrayi trees (97 v. 70cm). M. wrayi trees had greaterlateral root cross-sectional areas than D. muricatus treesalthough a greater proportion of this sectional area for D.muricatus was further down the soil profile. D.muricatus appeared to maintain relatively high water potentialsduring dry periods because of its access to deeper water supplies and thus itlargely avoided drought effects, but M. wrayi seemed to bemore affected yet tolerant of drought and was more plastic in its response. Theinteraction between water availability and topography determines these species'distributions and provides insights into how rain forests can withstandoccasional strong droughts.     

A molecular phylogeny and a revised classification of tribe Lepisoreae (Polypodiaceae) based on an analysis of four plastid DNA regions

Phylogenetic relationships within the palaeotropical tribe Lepisoroideae (Polypodiaceae) were investigated by studying sequence variation of four plastid DNA regions: rbcL, rps4 plus rps4‐trnS IGS, trnL intron plus trnL‐F IGS, rbcL‐atpB IGS plus part of atpB. In total, over 4000 nucleotides were sequenced for 39 species. Seven well‐supported clades were found in the analyses of the combined data set. We provide a new classification of Lepisoroideae by integrating phylogenetic results and known variation of morphological characters. The two small genera Neocheiropteris and Tricholepidium are supported as monophyletic, the genus Paragramma is resurrected and the genera Lepisorus, Neolepisorus, Lemmaphyllum and Lepidomicrosorium are re‐circumscribed. We proposed 14 new combinations, among which Caobangia is treated as a synonym of Lemmaphyllum. A key for identifying the recognized genera is presented. © 2010 The Linnean Society of London, Botanical Journal of the Linnean Society, 2010, 162 , 28–38.