Phylogenetic biogeography of the leafy liverwort Herbertus (Jungermanniales, Herbertaceae) based on nuclear and chloroplast DNA sequence data: correlation between genetic variation and geographical distribution

Aim The cosmopolitan genus Herbertus is notorious for having a difficult taxonomy and for the fact that there is limited knowledge of species ranges and relationships. Topologies generated from variable molecular markers are used to discuss biogeographical patterns in Herbertus and to compare them with the geological history of continents and outcomes reported for other land plants. Location Africa, Asia, Azores, Europe, southern South America, northern South America, North America, New Zealand. Methods Phylogenetic analyses of nuclear ribosomal internal transcribed spacer and chloroplast (cp) trnL–trnF sequences of 66 accessions of Herbertus and the outgroup species Triandrophyllum subtrifidum and Mastigophora diclados were used to investigate biogeographical patterns in Herbertus. Areas of putative endemism were defined based on the distribution of species included in the analyses. Maximum parsimony analyses were undertaken to reconstruct ancestral areas and intraspecies migration routes. Results The analyses reveal species‐level cladograms with a correlation between genetic variation and the geographical distribution of the related accessions. The southern South American Herbertus runcinatus is sister to the remainder of the genus, which is split into two main clades. One contains the Neotropical–African Herbertus juniperoideus and the New Zealand/Tasmanian Herbertus oldfieldianus. An African accession of H. juniperoideus is nested within Neotropical accessions. The second main clade includes species that inhabit Asia, the Holarctic, Africa, and northern South America. Maximum parsimony analyses indicate that this clade arose in Asia. Herbertus sendtneri originated in Asia and subsequently colonized the Holarctic and northern South America. An Asian origin and colonization into Africa is indicated for H. dicranus. Main conclusions The current distribution of Herbertus cannot be explained by Gondwanan vicariance. A more feasible explanation of the range is a combination of short‐distance dispersal, rare long‐distance dispersal events (especially into regions that faced floral displacements as a result of climatic changes) extinction, recolonization, and diversification. The African Herbertus flora is a mixture of Asian and Neotropical elements. Southern South America harbours an isolated species. The molecular data indicate partial decoupling of molecular and morphological variation in Herbertus. Biogeographical patterns in Herbertus are not dissimilar to those of other groups of bryophytes, but elucidation of the geographical ranges requires a molecular approach. Some patterns could be the result of maintenance of Herbertus in the inner Tropics during glacial maxima, and dispersal into temperate regions in warm phases.     

Cryptic speciation in Herbertus (Herbertaceae, Jungermanniopsida): Range and morphology of Herbertus sendtneri inferred from nrITS sequences

Maximum likelihood and parsimony analyses of nrITS1-5.8S-ITS2 sequences place Austrian Herbertus sendtneri in a well bootstrap supported clade with Herbertus azoricus and Neotropical accessions which were alternatively assigned to Herbertus subdentatus or Herbertus dicranus. Asian and African Herbertus dicranus form a separate lineage which is placed sister to several European Herbertus taxa. Herbertus borealis from the British Isles is placed sister to H. stramineus in a robust sister relationship, indicating that the species does not belong in the synonymy of H. dicranus. As a result of the molecular investigation, the range of Herbertus sendtneri is extended to the Neotropics and H. azoricus is placed into the synonymy of H. sendtneri. Without much doubt, Herbertus dicranus does not occur in tropical America. Morphologically, H. sendtneri and H. dicranus can at most be separated by weak tendencies. Herbertus sendtneri is characterized by the frequent occurrence of coarse appendages at the leaf margins and often completely papillose leaves. H. dicranus often has small appendages and a nearly smooth basal leaf half. Herbertus borealis, which is nonmonophyletic with H. dicranus in the molecular trees, cannot be separated morphologically from forms of H. dicranus with small appendages. Herbertus subdentatus is not identical with H. sendtneri. Morphological homoplasy and cryptic speciation are obviously common in Herbertus.We thank the owners and curators of the herbaria cited in the text for the loan of specimens, P. Schwartz for assistance with SEM techniques, and M. Lindner for help with laboratory work. M. Schmull, S.R. Gradstein, F.A. Hartmann, and R.-L. Zhu helped to collect Herbertus sendtneri. D.S. Rycroft (Glasgow) collected H. borealis. G. Gärtner and D. Miller kindly organized authorizations. Parts of this study were supported by the German Science Foundation (DFG grant HE 3584/1).     

Phylogenetic relationships and neotenic evolution of Metzgeriopsis (Lejeuneaceae) based on chloroplast DNA sequences and morphology

The systematic position of the enigmatic Asiatic liverwort Metzgeriopsis pusilla (Marchantiophyta), the single thalloid member of the largest family of leafy liverworts, Lejeuneaceae, was investigated based on sequences of the rbc L gene and the trn L-F region of chloroplast DNA, and morphology. Metzgeriopsis is not phylogenetically isolated from other taxa of Lejeuneaceae, as previously suggested, but is nested within Cololejeunea . The two genera share many morphological features, especially in the sporophyte generation, which is newly described. Metzgeriopsis and Cololejeunea are members of the Tuyamaella – Cololejeunea clade, characterized by neotenic features that probably evolved as adaptations to ephemeral habitats in tropical rain forests. Three different types of neoteny occur in this clade, which apparently originated by multiple heterochronic events. Within Lejeuneaceae, protonemal neoteny is unique to Metzgeriopsis and apparently resulted by evolution from a primary neotenic ancestor. The occurrence of protonemal neoteny in bryophytes is briefly reviewed and two types are recognized: species having a persistent thalloid protonema and species having a persistent filamentous protonema. The thalloid type is very rare and exclusive to epiphyllous liverworts, whereas the filamentous type is much more common and is characteristic of many terrestrial bryophytes, including the rare genus Protocephalozia . The new combination Cololejeunea metzgeriopsis (K.I.Goebel) comb. nov. is proposed.  © 2006 The Linnean Society of London, Botanical Journal of the Linnean Society , 2006, 151 , 293–308.     

Phylogeny of Rhaponticum (Asteraceae, Cardueae-Centaureinae) and related genera inferred from nuclear and chloroplast DNA sequence data: taxonomic and biogeographic implications

BACKGROUND AND AIMS: The precise generic delimitation of the Rhaponticum group is not totally resolved. The lack of knowledge of the relationships between the basal genera of Centaureinae could imply that genera whose position is as yet unresolved could belong to the Rhaponticum group. On the other hand, the affinities among the genera that are considered as members of this group are not well known. The aim of the study is to contribute to the phylogenetic and generic delineation of the Rhaponticum group on the basis of molecular data. METHODS: Parsimony and Bayesian analyses of the combined sequences of one plastid (trnL-trnF) and two nuclear (ITS region and ETS) molecular markers were carried out. The results of these analyses are discussed in the light of the biogeographic history. KEY RESULTS: The Rhaponticum group appears as monophyletic, and closely related to the genus Klasea. The results confirm the preliminary generic delimitation of the Rhaponticum group, with the new incorporation of the genus Centaurothamnus. Ochrocephala is supported as a separate genus from Rhaponticum and, contrary to this, Acroptilon and Leuzea appear as merged into the genus Rhaponticum. Several nomenclatural rearrangements are made in Klasea and Rhaponticum. CONCLUSIONS: The new molecular evidence is consistent with the morphological and karyological data, and suggests particularly coherent biogeographic routes of migration and speciation processes for the genus Rhaponticum. The biogeographic inference proposes a Near East and/or Caucasian origin for the genus. Furthermore, representatives of Rhaponticum could have reached Europe in two different ways: (1) expansion across central Asia to eastern Europe, and (2) expansion through the Near East, North Africa and then to the Iberian Peninsula and the Alps.     

Systematic affinities of Rhizophoraceae and Anisophylleaceae, and intergeneric relationships within Rhizophoraceae, based on chloroplast DNA, nuclear ribosomal DNA, and morphology

A cladistic analysis of sequences from the chloroplast gene rbcL was used to determine the systematic affinities of Rhizophoraceae and Anisophylleaceae. This analysis rejects close relationships of Rhizophoraceae with Celastraceae or Elaeocarpaceae, suggested previously, and identifies Erythroxylaceae as sister group within the Malpighiales, supported by several morphological and anatomical characters. Our molecular results also indicate that Anisophylleaceae are nested within Cucurbitales. Although this placement is novel, this affinity is also well supported by shared morphological characters. Tribal and generic relationships within Rhizophoraceae are evaluated with a combination of six molecular data sets (rbcL, atpB-rbcL intergenic spacer, trnL-trnF intergenic spacer, ITS1, ITS2, and 5.8S) and a morphological data set. These relationships are compared with results from previous morphological cladistic analyses. Against the background of the molecular results, we briefly discuss the evolution of morphological characters traditionally used for tribal subdivision as well as characters presumably significant for adaptation to mangrove habitats, namely, aerial stilt roots and vivipary.     

A morphological revision of the genus Herbertus S.Gray (Herbertaceae,Marchantiophyta) in Africa,including the East African islands

Abstract

The genus Herbertus S.Gray in Africa and the East African islands is revised. The division of the genus into two broad species complexes centred on H. dicranus (Tayl.ex Gottsche et al.) Trev. and H. juniperoideus (Sw.) Grolle is confirmed. H. capensis (Steph.) Sim, H. capillaris (Steph.) H. doggeltianus (Steph.) Demaret, H. lobatus (Steph.) Demaret, H. mascarenicus (Steph.) S.Arn., H. mollis (Steph.) Dusén, H. stuhlmannii (Steph.) Demaret and Schisma kilimandjarense Steph. are synonymous with H. dicranus. H. grossevittatus (Steph.) S.Arn. ex Grolle is synonymous with H. juniperoideus. Three new species are described: H. spicatus N.G.Hodgetts sp. nov., which is related to H. juniperoideus and appears close to the neotropical H. pensilis, with long, narrow leaf lobe apices and a sheathing leaf base; H. mauritianus N.G.Hodgetts sp. nov., also related to H. juniperoideus, has fewer basal slime papillae and the vitta bifurcating lower down; and H. pocsii N.G.Hodgetts sp. nov., which is related to H. dicranus but has setaceous leaf lobe apices composed of long, narrow cells. The relationships of the taxa and patterns of distribution, taking account of recent molecular work, are discussed.     

DNA barcoding of European Herbertus (Marchantiopsida, Herbertaceae) and the discovery and description of a new species

DNA barcoding of a group of European liverwort species from the genus Herbertus was undertaken using three plastid (matK, rbcL and trnH-psbA) and one nuclear (ITS) marker. The DNA barcode data were effective in discriminating among the sampled species of Herbertus and contributed towards the detection of a previously overlooked European Herbertus species, described here as H. norenus sp. nov. This species shows clear-cut differences in DNA sequence for multiple barcode regions and is also morphologically distinct. The DNA barcode data were also useful in clarifying taxonomic relationships of the European species with some species from Asia and North America. In terms of the discriminatory power of the different barcode markers, ITS was the most informative region, followed closely by matK. All species were distinguishable by ITS alone, rbcL + matK and various other multimarker combinations.     

九子母属的系统位置：来自叶绿体rbcL序列及核核糖体ITS序列的证据

九子母属Dobinea Buch-Ham.ex D.Don是一个东亚特有属,包含贡山九子母D.vulgaris Buch-Ham.ex D.Don和羊角天麻D.delavayi(Baill.)Baill.两种,主要分布于中国两南地区.有关九子母属的系统位置长期存在争议,小同的学者曾将其归入漆树科Anacardiaceae、无忠子科sapindaceae和九子母科Podoaceae.本文基于rbcL和ITs探讨了其系统位置,结果表明,九子母属的两个种自成单系,并且是漆树科的成员.     

A taxonomic revision and pollen morphology of the genus Dendrokingstonia (Annonaceae)

The genus Dendrokingstonia (Annonaceae) is taxonomically revised and palynologically studied. Three species are recognized, one of which, D. gardneri , is described as new to science. One new combination, D. acuminata , is made. The genus occurs from southern Thailand to Peninsular Malaysia and Sumatra. On the basis of macromorphology and pollen characters, it is considered to be related to Monocarpia. Both genera show a combination of macromorphological characters that is rare in the family, i.e. considerably enlarged stigmas, leaves with percurrent tertiary veins, a highly reduced number of carpels per flower and relatively large monocarps with a thick, hard wall. Scanning and transmission electron microscopy show that the pollen grains of Dendrokingstonia and Monocarpia are monosulcate monads with a columellate infratectum and a more or less bulging intine at the sulcus. © 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2012, 168 , 76–90.     

Molecular phylogeny ofForsythia (Oleaceae) based on chloroplast DNA variation

Phylogenetic relationships of ten wild species and several cultivars ofForsythia were reconstructed based on the chloroplast (cp) DNA variation. A total of 216 cpDNA variants, 44 of which were potentially phylogenetically informative, was detected using 24 restriction endonucleases. Phylogenetic analysis usingFontanesia andAbeliophyllum as outgroups revealed four well defined species groups in the genus: 1)F. suspensa, 2)F. europaea — F. giraldiana, 3)F. ovata — F. japonica — F. viridissima, and 4)F. koreana — F. manshurica — F. saxatilis. The amount of support for each monophyletic group was evaluated by various methods including character number, decay analysis, parsimony bootstrapping, Neighbour-Joining (NJ) — bootstrapping, NJ-jackknifing, and the topology-dependent permutation tail probability (T-PTP) test. The data do not support the hybrid origin ofF. intermedia fromF. suspensa andF. viridissima. The disjunctly distributed European species,F. europaea, was identified as a sister species of the ChineseF. giraldiana and it was probably derived through recent long distance dispersal.     

Phylogenetic relationships in Bulbostylis (Abildgaardieae: Cyperaceae) inferred from nuclear and plastid DNA sequence data

Previous molecular phylogenetic analyses of the family Cyperaceae based on rbcL sequences showed Bulbostylis as paraphyletic, with B. atrosanguinea and B. hispidula forming a clade with Nemum spadiceum. On the contrary, phylogenetic analyses of the tribe Abildgaardieae based on nuclear (ITS ribosomal region) and plastid sequences (trnL-F region) showed Bulbostylis as monophyletic, although they only incorporated four species of Bulbostylis and none of Nemum. In this work, we presented a phylogenetic hypothesis of Bulbostylis based on a comprehensive sampling, including species from different continents for the first time. New sequences of Abildgaardia, Crosslandia, Fimbristylis, and Nemum were included to test the monophyly of Bulbostylis. In total, 84 sequences of both ITS and trnL regions were generated. Analyses were performed using Bayesian inference, maximum likelihood, and parsimony. Ancestral state reconstruction was performed using ML, MCMC, and parsimony methods. In all analyses, Bulbostylis resulted paraphyletic as Nemum atracuminatum is nested within it. Most American species of Bulbostylis grouped together, but relationships amongst them appeared poorly resolved. Ancestral state reconstructions of native distribution suggest an African ancestor of Bulbostylis, with at least three introduction independent events of the species in America. Morphological diagnostic characters such as the ‘style base permanence or detachment from the ripe achene’, and the ‘micromorphological patterns of the achene surface’ are homoplastic in this phylogenetic context, and therefore unsuitable to propose infrageneric groupings within the Bulbostylis.     

Phylogenetic analysis of the genus Hexachlamys (Myrtaceae) based on plastid and nuclear DNA sequences and their taxonomic implications

Myrtaceae are one of the most species‐rich families of flowering plants in the Neotropics. They include several complex genera and species; Hexachlamys is one of the complex genera. It has not been recognized as a distinct genus and has been included in Eugenia, based on morphological grounds. Therefore, molecular systematic studies may be useful to understand and to help to solve these relationships. Here, we performed a molecular phylogenetic analysis using plastid and nuclear data in order to check the inclusion of Hexachlamys in Eugenia. Plastid (accD, rpoB, rpoC1, trnH‐psbA) and nuclear (ITS2) sequence data were analysed using Bayesian and maximum parsimony methods. The trees constructed using ITS2 and trnH‐psbA were the best able to resolve the relationships between species and genera, revealing the non‐monophyly of Hexachlamys. The molecular phylogenetic analyses were in agreement with previous morphological revisions that have included Hexachlamys in Eugenia. These results reinforce the importance of uniting knowledge and strategies to understand better issues of delimitation of genera and species in groups of plants with taxonomic problems. © 2013 The Linnean Society of London, Botanical Journal of the Linnean Society, 2013, 172 , 532–543.     

Acceptance of Liochlaena Nees and Solenostoma Mitt., the systematic position of Eremonotus Pearson and notes on Jungermannia L. s.l. (Jungermanniidae) based on chloroplast DNA sequence data

Nucleotide sequence variation of the chloroplast rbcL gene of 78 representatives of Jungermanniales suborders Jungermanniineae and Cephaloziineae and five outgroup species is analysed using maximum parsimony and maximum likelihood. Jungermannia s.l. is resolved in three independent lineages corresponding to Jungermannia subgen. Jungermannia, Liochlaena and Solenostoma (incl. subgen. Plectocolea). Based on the outcome of the phylogenetic analyses we adopt a narrow generic concept of Jungermannia and accept the genera Liochlaena and Solenostoma. Contrary to proposed hypotheses, the monospecific genus Eremonotus is not nested in Scapaniaceae, Gymnomitriaceae, Cephaloziellaceae or Cephaloziaceae but placed in a clade together with Jungermannia s.str., Liochlaena, Delavayella and Leiocolea. These genera possess female involucres consisting solely of leaf tissue (perianths). Related clades comprise genera with female involucres originating at least partly from stem tissue. We propose to include Delavayella, Eremonotus, Jungermannia s.str., Leiocolea and Liochlaena in Jungermanniaceae based on the phylogenetic reconstructions of cpDNA variation and the distribution of perianths in Jungermanniales suborder Jungermanniineae.     

A phylogenetic analysis of American Zamiaceae (Cycadales) using chloroplast DNA restriction fragment length polymorphisms

A phylogenetic analysis of American cycad genera, all belonging to the family Zamiaceae, was attempted using chloroplast DNA restriction fragment polymorphisms.Ceratozamia mexicana Brongn.,Chigua restrepoi D. Stevenson,Dioon edule Lindley,Microcycas calocoma (Miq.) A. DC.,Zamia fischeri Miq., andZamia skinneri Warsz. ex A. Dietrich were used as representatives of the genera.Cycas revoluta Thunb., belonging to the family Cycadaceae, was used as an outgroup, following previous morphological works. One hundred and forty-one shared restriction fragments were scored for presence/absence and both Wagner and Dollo parsimony analyses were performed. The single, fully resolved, most parsimonious trees obtained from the analyses were topologically identical and perfectly matched previous morphology-based phylogenetic hypotheses. Statistical evaluation of the data showed a good reliability for the obtained phylogeny.Dioon edule, belonging to a different subfamily and more primitive on morphological grounds, proved to be the most primitive among American cycads as inferred from the molecular data;Chigua restrepoi, never analyzed before on cladistic grounds, was found to be the sister group of the genusZamia.     

A nuclear DNA phylogeny and proposed taxonomic revision of African greenbuls (Aves, Passeriformes, Pycnonotidae)

The Pycnonotidae (bulbuls and greenbuls) comprise approximately 130 species and are widely distributed across Africa and Asia, mainly in evergreen thickets and forest. Recent molecular findings suggest a basal split between the African and the Asian species, although the three African Pycnonotus species are part of the Asian radiation and represent a relative recent immigration to Africa. In this study we investigate the phylogenetic relationships within the African clade, which with the exclusion of Pycnonotus contains approximately 50 species, of which the majority are placed in three large genera Andropadus , Phyllastrephus and Chlorocichla . We use three nuclear markers (myoglobin intron 2, ODC introns 6 and 7 along with intervening exon 7, and β-fibrinogen intron 5), together encompassing 2072 aligned positions, to infer the relationships within the African clade. The resulting tree is generally well supported and indicates that none of the three largest currently recognized genera are monophyletic. For instance, the species included in Andropadus represent three different clades that are not each other's closest relatives. The montane species currently placed in that genus form a strongly supported clade, which is sister to Ixonotus , Thescelocichla, Baeopogon and Chlorocichla , although within this clade the genus Chlorocichla is polyphyletic. The remaining Andropadus species fall into two groups, one of these with A . importunus and A . gracilirostris , which along with Calyptocichla serina form a basal branch in the African greenbul radiation. In support of some previous studies the Leaf-love ( Pyrrhurus scandens ) is placed within Phyllastrephus . We also propose a new classification that reflects the phylogenetic relationships among African greenbuls.     

Phylogenetic relationships and the maternal donor of Roegneria (Triticeae: Poaceae) based on three nuclear DNA sequences (ITS,Acc1, and Pgk1) and one chloroplast region (trnL-F)

Roegneria is a polyploid perennial genus in the tribe Triticeae. Some species of Roegneria are morphologically similar to genus Elymus and have been classified in Elymus. To investigate the delimitation and phylogenetic relationships of Roegneria, nuclear (ITS, Acc1, and Pgk1) and chloroplast (trnL–trnF) DNA regions were sequenced for 38 allopolyploid species and 32 diploid species of Triticeae. Phylogenetic analyses of nuclear DNA revealed that all Roegneria species were included in the St and Y genome clades, and that the Y genome was closely related to the V and Xp genomes. The chloroplast DNA dataset showed that Roegneria species were grouped with Pseudoroegneria species. The Pseudoroegneria species from the Middle East (P. libanotica and P. tauri) and Central Asia (P. strigosa) were more closely related to Roegneria species. The results suggested that: (i) the species containing the St and Y genomes should be segregated from Elymus and treated as a distinct genus, Roegneria, based on the genomic constitution; (ii) P. libanotica, P. tauri, and/or P. strigosa potentially served as the maternal donor of the St genome in Roegneria; (iii) The Y genome of Roegneria originated from a diploid Y genome species, and the V and Xp genomes may have contributed to Y genome formation; (iv) among Roegneria species of previously uncertain genomic constitution, R. seriotina was tetraploid and possessed the StY genomes, E. calcicolus was hexaploid with the StYH genomic constitution and should be classified in Campeiostachys, R. glaucifolia possessed the StStY genomes, and R. tschimganica had the genomic constitution St₁St₂Y.