Phylogeny and taxonomy of the Pyrenaria complex (Theaceae) based on nuclear ribosomal ITS sequences

The generic limits in the Pyrenaria complex are discussed based on morphological and molecular evidence. The phylogeny of the Pyrenaria complex was reconstructed using parsimony and Bayesian analyses of sequence data from the nuclear internal transcribed spacer (ITS) region. The Pyrenaria complex is shown to be monophyletic and is sister to the Camellia–Polyspora clade. None of the previously recognized genera (including Pyrenaria, Tutcheria, Parapyrenaria and Sinopyrenaria) is monophyletic, and the species of these genera are scattered and nested within the Pyrenaria complex, suggesting that the four genera should be combined as Pyrenaria sensu lato. This study indicates a close relationship among the genera within the Pyrenaria complex, Camellia and Polyspora, and reveals that Camellia has a closer relationship with Polyspora than with the Pyrenaria complex.     

The phylogenetic position of Apterosperma (Theaceae) based on morphological and karyotype characters

Classifications of Theaceae have usually placed the endangered monotypic genus Apterosperma in tribe Schimeae (x=18), whereas recent molecular phylogenetic evidence supports its transfer to tribe Theeae (x=15). Molecular data have not resolved the phylogenetic position of Apterosperma within Theeae. We investigated the chromosome number and karyotype of Apterosperma in the context of molecular and morphological phylogenetic evidence to provide further insight into the placement of Apterosperma within Theaceae. The chromosome number and karyotype was found to be 2n = 30 = 26m + 4sm, consistent with the transfer of Apterosperma to tribe Theeae. When the chromosome data were incorporated into a data set of 46 other nonmolecular characters, Apterosperma was placed as the first-diverging lineage within the clade comprising tribe Theeae. This supports its placement based on molecular data. The low intrachromosomal asymmetry (type 1A) of Apterosperma, presumably ancestral for the family, is also consistent with this placement. Character optimization strongly supports a base chromosome number of x=15 for tribe Theeae. Because of variable and sometimes conflicting chromosome count reports of species in tribes Schimeae and Stewartieae, the base chromosome number of Theaceae could be either x=15 or 17.     

The Chloroplast Genome of Hyoscyamus niger and a Phylogenetic Study of the Tribe Hyoscyameae (Solanaceae)

The tribe Hyoscyameae (Solanaceae) is restricted to Eurasia and includes the genera Archihyoscyamus, Anisodus, Atropa, Atropanthe, Hyoscyamus, Physochlaina, Przewalskia and Scopolia. Even though the monophyly of Hyoscyameae is strongly supported, the relationships of the taxa within the tribe remain unclear. Chloroplast markers have been widely used to elucidate plant relationships at low taxonomic levels. Identification of variable chloroplast intergenic regions has been developed based on comparative genomics of chloroplast genomes, but these regions have a narrow phylogenetic utility. In this study, we present the chloroplast genome sequence of Hyoscyamus niger and make comparisons to other solanaceous plastid genomes in terms of gene order, gene and intron content, editing sites, origins of replication, repeats, and hypothetical open reading frames. We developed and sequenced three variable plastid markers from eight species to elucidate relationships within the tribe Hyoscyameae. The presence of a horizontally transferred intron in the mitochondrial cox1 gene of some species of the tribe is considered here a likely synapomorphy uniting five genera of the Hyoscyameae. Alternatively, the cox1 intron could be a homoplasious character acquired twice within the tribe. A homoplasious inversion in the intergenic plastid spacer trnC-psbM was recognized as a source of bias and removed from the data set used in the phylogenetic analyses. Almost 12 kb of plastid sequence data were not sufficient to completely resolve relationships among genera of Hyoscyameae but some clades were identified. Two alternative hypotheses of the evolution of the genera within the tribe are proposed.     

EVIDENCE FOR A CLOSE RELATIONSHIP BETWEEN IOSTEPHANE AND VIGUIERA (ASTERACEAE: HELIANTHEAE)

The phylogenetic relationship of Iostephane is assessed using data from morphology, flavonoid chemistry, and chloroplast DNA and nuclear ribosomal DNA restriction fragment analysis. Morphological evidence supports placement of Iostephane in subtribe Helianthinae, but fails to clarify the placement of the genus within this assemblage. Further evidence for the placement of Iostephane in subtribe Helianthinae is provided by the presence in all species of the genus of floral flavonoids of the chalcone/aurone type, which provides a distinctive trait for the subtribe within the tribe Heliantheae. Analysis of chloroplast DNA from two species of Iostephane, I. heterophylla and I. madrensis, in comparison to Viguiera and related genera indicates that the restriction site patterns with 16 enzymes for the Iostephane species are virtually identical to one another as well as to those of Viguiera sect. Maculatae. Data from restriction fragment patterns of nuclear rDNA are concordant with the results from chloroplast DNA in suggesting a direct relationship between the two groups. The close phylogenetic relationship between Iostephane and Viguiera sect. Maculatae suggested by the DNA restriction fragment data was not suggested by any other set of data.     

Molecular phylogeny and systematics of the tribe Chorisporeae (Brassicaceae)

Sequence data from nuclear (ITS) and chloroplast (trnL-F) regions for 89 accessions representing 56 out of 64 species from all five genera of the tribe Chorisporeae (plus Dontostemon tibeticus) have been studied to test the monophyly of the tribe and its component genera, clarify its boundaries, and elucidate its phylogenetic position in the family. Both data sets showed strong support for the monophyly of the Chorisporeae as currently delimited, though the position of its tentative member D. tibeticus was not resolved by ITS. Parrya and Pseudoclausia are poly- and paraphyletic with regard to each other, and Chorispora is either polyphyletic or at least paraphyletic (comprising Diptychocarpus) within a weakly supported monophyletic clade. The incongruence in branching pattern among the markers was most likely caused by hybridization and possibly influenced by incomplete lineage sorting. The present results suggest uniting Pseudoclausia, Clausia podlechii, and Achoriphragma with Parrya and transferring P. beketovii and P. saposhnikovii to Leiospora (Euclidieae). We also obtained support for splitting Chorispora into two geographically defined groups, one of which is closer to Diptychocarpus. Both data sets revealed a close relationship of the Chorisporeae to Dontostemoneae, while ITS also indicated affinity to Hesperideae. Therefore, the position of Chorisporeae needs further verification.     

Multiple species of wild tree peonies gave rise to the ‘king of flowers’, Paeonia suffruticosa Andrews

The origin of cultivated tree peonies, known as the ‘king of flowers'' in China for more than 1000 years, has attracted considerable interest, but remained unsolved. Here, we conducted phylogenetic analyses of explicitly sampled traditional cultivars of tree peonies and all wild species from the shrubby section Moutan of the genus Paeonia based on sequences of 14 fast-evolved chloroplast regions and 25 presumably single-copy nuclear markers identified from RNA-seq data. The phylogeny of the wild species inferred from the nuclear markers was fully resolved and largely congruent with morphology and classification. The incongruence between the nuclear and chloroplast trees suggested that there had been gene flow between the wild species. The comparison of nuclear and chloroplast phylogenies including cultivars showed that the cultivated tree peonies originated from homoploid hybridization among five wild species. Since the origin, thousands of cultivated varieties have spread worldwide, whereas four parental species are currently endangered or on the verge of extinction. The documentation of extensive homoploid hybridization involved in tree peony domestication provides new insights into the mechanisms underlying the origins of garden ornamentals and the way of preserving natural genetic resources through domestication.     

First phylogenetic analysis of the tribe Oligaphorurini (Collembola: Onychiuridae) inferred from morphological data,with implications for generic classification

Oligaphorurini represent tribe of the subfamily Onychiurinae, which currently comprises 5 genera and 53 species. The present study evaluated the monophyly of Oligaphorurini genera. We investigated phylogenetic relationships among 39 species, representing all extant genera of Oligaphorurini. Both equal- and implied-weighting parsimony analyses were used in phylogenetic reconstruction. The cladistic analyses were based on comprehensive survey of adults’ morphological characters because specimens suitable for molecular studies were not available for the majority taxa. The phylogenetic analysis resulted in the recognition of a monophyletic Chribellphorura, and strongly supported non-monophyly of the previously recognized genera Archaphorura, Dimorphaphorura, Micraphorura, and Oligaphorura. The following new synonymy is recognized: Oligaphorura = Dimorphaphorura syn. nov., = Micraphorura syn. nov., = Archaphorura syn. nov. The general classification of Oligaphorurini is followed by the diagnoses of genera and key to the all known species.     

Phylogeny and evolutionary divergence times in Apterosperma and Euryodendron: Evidence of a Tertiary origin in south China

Apterosperma and Euryodendron, monotypic genera in Theaceae (sensu lato), are endemic and restrictedly distributed in south China. The two genera are not included in the major classification systems. However, their systematic position and origin have been subject to intense debate in the last decade. In this study, the phylogeny and divergence times of both Apterosperma and Euryodendron were inferred using combined dataset of chloroplast DNA trnL-F and atpB-rbcL non-coding sequences and nrDNA ITS sequences. The results from Bayesian inference, maximum parsimony, and maximum likelihood consistently showed that (i) Euryodendron is a valid genus, which is closer to Eurya than to Cleyera and (ii) Apterosperma is a genus of the tribe Theeae along with Tutcheria and Camellia. It was first reported that the divergence time of Apterosperma was 61.98 million years ago (mya), whereas that of Euryodendron 20.51 mya, indicating Tertiary origins in south China. The divergence of Apterosperma appears to be the result of increased ecological opportunity after Cretaceous/Tertiary extinction events and related with high temperatures and high humidity environments. By contrast, the origin of Euryodendron may be associated with historical mountain building events as well as the significant climate changes that established cooler temperatures prevailing until today.     

Tribal assignment of <Emphasis Type="Italic">Heldreichia</Emphasis> Boiss. (Brassicaceae): evidence from nuclear ITS and plastidic <Emphasis Type="Italic">ndh</Emphasis>F markers

Heldreichia Boiss. is a monospecific genus mainly distributed in Anatolia and the Lebanon. Although morphological variation and infrageneric phylogenetic relationships were recently studied in detail, Heldreichia remained as one of the few orphan genera that have not yet been assigned to any tribe. In the current study, we used sequence data from the nuclear ITS and chloroplast ndhF regions of Heldreichia and representatives of main Brassicaceae lineages and tribes to determine its tribal affiliation. Bayesian-based phylogenetic analyses clearly show with high support that Heldreichia is a member of the recently expanded tribe Biscutelleae. Furthermore, we characterize the tribe Biscutelleae morphologically and provide a determination key for all its genera.     

Exon primed intron-crossing (EPIC) markers reveal natural hybridization and introgression in Actinidia (Actinidiaceae) with sympatric distribution

Interspecific hybridization is widespread among plants. Understanding the phylogenetic relationships among species is necessary for revealing the potential hybridization events. Actinidia, best known as kiwifruit genus found throughout a wide range in eastern Asian from Indonesia to Siberia. In this study, phylogenetic relationships of Actinidia species with sympatric distributions were investigated using three chloroplast introns (trnL-F, atpB-rbcL and rpl32-trnL) and three Exon primed intron-crossing (EPIC) markers. Chloroplast phylogeny supports non-monophyly of the five species studied excluding Actinidia fulvicoma var. lanata. The non-monophyly was also revealed by EPIC markers. Our results showed EPIC markers are more variable and informative for phylogenetic inference than that of chloroplast markers. The incongruences between loci from the plastid and nuclear DNA phylogenic trees may stem from incomplete lineage sorting or historical introgression hybridization. Incomplete lineage sorting may explain the non-monophyly between Actinidia chrysantha (section Maculatae) and other four species (section Stellatae), and introgression hybridization and high level of interspecific gene flow may explain the non-monophyly among the species of sect. Stellatae. Thus, natural hybridization and introgression may be common in Actinidia with sympatric distribution.     

Phylogenetic relationships in tribe Spiraeeae (Rosaceae) inferred from nucleotide sequence data

Tribe Spiraeeae has generally been defined to include Aruncus, Kelseya, Luetkea, Pentactina, Petrophyton, Sibiraea, and Spiraea. Recent phylogenetic analyses have supported inclusion of Holodiscus in this group. Spiraea, with 50-80 species distributed throughout the north temperate regions of the world, is by far the largest and most widespread genus in the tribe; the remaining genera have one to several species each. Phylogenetic analyses of nuclear ITS and chloroplast trnL-trnF nucleotide sequences for 33 species representing seven of the aforementioned genera plus Xerospiraea divided the tribe into two well supported clades, one including Aruncus, Luetkea, Holodiscus, and Xerospiraea, the second including the other genera. Within Spiraea, none of the three sections recognized by Rehder based on inflorescence morphology is supported as monophyletic. Our analyses suggest a western North American origin for the tribe, with several biogeographic events involving vicariance or dispersal between the Old and New Worlds having occurred within this group.     

Molecular phylogeny of Cotoneaster (Rosaceae) inferred from nuclear ITS and multiple chloroplast sequences

Cotoneaster Medik. (Rosaceae, Maloideae) is distributed in Europe, North Africa, and temperate areas of Asia except Japan. Members of the genus exhibit considerable morphological variation. The infrageneric classification is also obscured by polyploidy, hybridization, and apomixis. In this study, phylogenetic analyses were conducted to test infrageneric classifications of this genus using DNA sequence data from the nuclear ITS (nrITS) region and three chloroplast intergenic spacer regions. Maximum parsimony and Bayesian inference analyses of both datasets agreed with the two sections/subgenera of Koehne’s classification system, and suggested that four subsections (Microphylli, Chaenopetalum, Adpressi, and Cotoneaster) and the series of Koehne’s classification system were non-monophyletic. The incongruence length difference test indicated that the nrITS and cpDNA datasets were significantly incongruent (P = 0.001), and the placement of 14 species was discordant in phylogenetic trees derived from the two datasets. Within Cotoneaster, hybridization was indicated to be an important factor contributing to the incongruence between the nrITS and cpDNA data. By mapping nine morphological characters onto the combined nrITS–cpDNA phylogenetic tree, we inferred that a deciduous habit, glabrous fruit, white anthers, erect and light pink petals, and white filaments are plesiomorphic character states in Cotoneaster.     

Comparative Chloroplast Genomes of Camellia Species

Background

Camellia , comprising more than 200 species, is a valuable economic commodity due to its enormously popular commercial products: tea leaves, flowers, and high-quality edible oils. It is the largest and most important genus in the family Theaceae. However, phylogenetic resolution of the species has proven to be difficult. Consequently, the interspecies relationships of the genus Camellia are still hotly debated. Phylogenomics is an attractive avenue that can be used to reconstruct the tree of life, especially at low taxonomic levels.

Methodology/Principal Findings

Seven complete chloroplast (cp) genomes were sequenced from six species representing different subdivisions of the genus Camellia using Illumina sequencing technology. Four junctions between the single-copy segments and the inverted repeats were confirmed and genome assemblies were validated by PCR-based product sequencing using 123 pairs of primers covering preliminary cp genome assemblies. The length of the Camellia cp genome was found to be about 157kb, which contained 123 unique genes and 23 were duplicated in the IR regions. We determined that the complete Camellia cp genome was relatively well conserved, but contained enough genetic differences to provide useful phylogenetic information. Phylogenetic relationships were analyzed using seven complete cp genomes of six Camellia species. We also identified rapidly evolving regions of the cp genome that have the potential to be used for further species identification and phylogenetic resolution.

Conclusions/Significance

In this study, we wanted to determine if analyzing completely sequenced cp genomes could help settle these controversies of interspecies relationships in Camellia . The results demonstrate that cp genome data are beneficial in resolving species definition because they indicate that organelle-based “barcodes”, can be established for a species and then used to unmask interspecies phylogenetic relationships. It reveals that phylogenomics based on cp genomes is an effective approach for achieving phylogenetic resolution between Camellia species.     

Tribe Eritrichieae (Boraginaceae s.str.) in West Asia: a molecular phylogenetic perspective

A selection of Boraginaceae genera was used to obtain a framework for the phylogenetic position of some tribes belong to subfamily Boraginoideae and genera within tribe Eritrichieae (Heterocaryum, Rochelia, Eritrichium, Lappula, Lepechiniella, and Asperugo) and related species. Our results were produced on the basis of nrDNA ITS and cpDNAtrnL-F sequences. The combined nrDNA ITS trnL-F data confirm four main clades of Boraginoideae comprising Echiochileae, Boragineae, Lithospermeae, and Cynoglosseae s. l. (including Eritrichieae, Cynoglosseae s. str., and Myosotideae). The tribe Eritrichieae itself at the current status is paraphyletic; some members, for example Asperugo procumbens, Lepechiniella inconspicua, Myosotidium hortensia, and Cryptantha flavoculata are placed out of the core tribe Eritrichieae. The genus Heterocaryum is monophyletic and allied with a subclade of genera Lappula, Lepechiniella, Eritrichium, and Rochelia. Rochelia is monophyletic, but Eritrichium and Lappula are non-monophyletic. Lepechiniella is nested among a group of Lappula species.     

Taxonomic Study of Korean <Emphasis Type="Italic">Scirpus</Emphasis> L. s.l. (Cyperaceae) II: Pattern of Phenotypic Evolution Inferred from Molecular Phylogeny

Scirpus L. s.l. is well known as one of the polyphyletic groups in Cyperaceae. Recent molecular phylogenetic studies clearly suggested that Scirpus s.l. should be separated into several independent genera. In this study, we intend to present the morphological variations and patterns of phenotypic evolution based on molecular phylogeny of Korean Scirpus s.l. Five genera, including 21 taxa from Korean Scirpus s.l., were examined: three species of Bolboschoenus, three species of Schoenoplectus, eight species of Schoenoplectiella including one hybrid, five species of Scirpus, and two species of Trichophorum. For morphological analyses, 23 and 48 characters were selected from vegetative and reproductive organs, respectively. Molecular phylogeny was inferred from a nuclear ribosomal internal transcribed spacer, the chloroplast rbcL gene, and the chloroplast trnL-F region. Distinct characteristics and quantitative variation was presented for identification of the five genera and their species. A pronounced pattern of morphological character change was reduction, although many other character states seem to be homoplastic. We suggest that the reduction of phenotypic characteristics has been expressed in terms of condensation of internodes, reduction of leaf blade, and simplification of inflorescence among five genera of Korean Scirpus s.l.     

Genus-level phylogeny of snakes reveals the origins of species richness in Sri Lanka

Snake diversity in the island of Sri Lanka is extremely high, hosting at least 89 inland (i.e., non-marine) snake species, of which at least 49 are endemic. This includes the endemic genera Aspidura, Balanophis, Cercaspis, Haplocercus, and Pseudotyphlops, which are of uncertain phylogenetic affinity. We present phylogenetic evidence from nuclear and mitochondrial loci showing the relationships of 40 snake species from Sri Lanka (22 endemics) to the remaining global snake fauna. To determine the phylogenetic placement of these species, we create a molecular dataset containing 10 genes for all global snake genera, while also sampling all available species for genera with endemic species occurring in Sri Lanka. Our sampling comprises five mitochondrial genes (12S, 16S, cyt-b, ND2, and ND4) and five nuclear genes (BDNF, c-mos, NT3 RAG-1, and RAG-2), for a total of up to 9582 bp per taxon. We find that the five endemic genera represent portions of four independent colonizations of Sri Lanka, with Cercaspis nested within Colubrinae, Balanophis in Natricinae, Pseudotyphlops in Uropeltidae, and that Aspidura + Haplocercus represents a distinct, ancient lineage within Natricinae. We synonymize two endemic genera that render other genera paraphyletic (Haplocercus with Aspidura, and Cercaspis with Lycodon), and discover that further endemic radiations may be present on the island, including a new taxon from the blindsnake family Typhlopidae, suggesting a large endemic radiation. Despite its small size relative to other islands such as New Guinea, Borneo, and Madagascar, Sri Lanka has one of the most phylogenetically diverse island snake faunas in the world, and more research is needed to characterize the island’s biodiversity, with numerous undescribed species in multiple lineages.     

Polyphyly of the grass tribe Hainardieae (Poaceae: Pooideae): identification of its different lineages based on molecular phylogenetics, including morphological and cytogenetic characteristics

The small pooid grass tribe Hainardieae comprises six genera with approximately ten species; however, this tribe was not accepted by all previous taxonomic treatments. To study the relationships among these genera and to infer the phylogeny and evolutionary patterns, we used sequence variation of the internal transcribed spacers (ITS) of nuclear ribosomal and chloroplast (cp) matK DNA and morphology. Many genera of the Aveneae/Poeae tribe complex additionally were included. Both molecular datasets showed Hainardieae to be highly polyphyletic, and its genera to branch with different groups of the Aveneae/Poeae. Parapholis and Hainardia are corroborated as being closely related, and belonging to a firmly supported Eurasian clade together with Catapodium incl. Scleropoa, Cutandia, Desmazeria, Sphenopus, Vulpiella (subtribe Parapholiinae) and with Cynosurus as sister to this assemblage. The other genera of traditionally recognised Hainardieae are positioned phylogenetically distant: Mediterranean Narduroides is verified as more or less related to Festuca and relatives (subtribe Loliinae), whereas the west Eurasian Pholiurus is close to the lineage of Poa and relatives (subtribe Poinae). North American Scribneria is sister to Deschampsia and both genera should be unified under a common subtribe (Aristaveninae or Holcinae). The phylogenetic position of the Algerian genus Agropyropsis (close to Narduroides and within the Loliinae) is suggested on morphology only, because no molecular data was obtained for it. Considering classification, we support the abandonment of tribe Hainardieae and argue to abandon Poeae subtribe Scribneriinae. Poeae subtribe Parapholiinae is redefined with a novel genus content, due to the exclusion of Agropyropsis and Pholiurus and the inclusion of Vulpiella.