cpDNA Datasets Research Articles

Mallomonas gemina comb. et stat. nov. (Synurales, Chrysophyceae)—a new combination based on molecular studies

Strains of Mallomonas favosa f. favosa and Mallomonas favosa f. gemina from Vietnam have been studied. Their phylogenetic position was revealed using the SSU rDNA + rbcL cpDNA dataset. The ultrastructure of the scales and bristles was studied using transmission and scanning electron microscopy. A new combination was proposed: Mallomonas gemina comb. et stat. nov. The morphological features of the species are discussed in this paper. Based on a revision of the published data, the distribution of Mallomonas gemina was clarified. Mallomonas gemina is recorded mainly in tropical and subtropical areas in Asia.

Morphology, phylogenetic position and distribution of Mallomonas mangofera and Mallomonas foveata comb. et stat. nov. (Synurales, Chrysophyceae)

Strains of Mallomonas mangofera var. mangofera and M. mangofera var. foveata from Russia and Vietnam were studied. Their phylogenetic position was revealed using the SSU rDNA + rbcL cpDNA dataset. The ultrastructure of scales and bristles was studied using transmission and scanning electron microscopy. Based on these studies, a new combination was proposed: Mallomonas foveata comb. et stat. nov. The problems associated with the identification of Mallomonas mangofera and determination of the scale morphotype belonging to this taxon are discussed, and a new emended formal description and holotype are proposed. Based on the literature data and metabarcoding results, the distribution of Mallomonas mangofera and Mallomonas foveata was revised. Mallomonas mangofera has been recorded mainly in the temperate zone of Eurasia, North America and Japan. Mallomonas foveata has a wider distribution and is more often observed in regions with a warm climate.

Evolutionary history of an Irano-Turanian cushion-forming legume (Onobrychis cornuta).

The Irano-Turanian region is one of the largest floristic regions in the world and harbors a high percentage of endemics, including cushion-like and dwarf-shrubby taxa. Onobrychis cornuta is an important cushion-forming element of the subalpine/alpine flora of the Irano-Turanian floristic region. To specify the genetic diversity among the populations of this species (including individuals of O. elymaitica), we employed nrDNA ITS and two noncoding regions of plastid DNA (rpl32-trnL(UAG) and trnT(UGU)-trnL(UAA)). The most striking feature of O. cornuta assemblages was the unexpectedly high nucleotide diversity in both the nDNA and cpDNA dataset. In the analyses of nuclear and plastid regions, 25 ribotypes and 42 haplotypes were found among 77 and 59 accessions, respectively, from Iran, Turkey, and Afghanistan. Network analysis of the datasets demonstrated geographic differentiation within the species. Phylogenetic analyses of all dataset retrieved O. cornuta as a non-monophyletic species due to the inclusion of O. elymaitica, comprising four distinct lineages. In addition, our analyses showed cytonuclear discordance between both nuclear and plastid topologies regarding the position of some O. cornuta individuals. The underlying causes of this inconsistency remain unclear. However, we speculate that chloroplast capture, incomplete lineage sorting, and introgression were the main reasons for this event. Furthermore, molecular dating analysis indicated that O. cornuta originated in the early Pliocene (around 4.8 Mya) and started to diversify throughout the Pliocene and in particular the Pleistocene. Moreover, O. elymaitica was reduced to a subspecific rank within the species.

Phylogeography and ecological niche modeling implicate multiple microrefugia of Swertia tetraptera during quaternary glaciations

BackgroundClimate fluctuations during the Pleistocene and mountain uplift are vital driving forces affecting geographic distribution. Here, we ask how an annual plant responded to the Pleistocene glacial cycles.MethodsIn this study, we analyzed the population demographic history of the annual herb Swertia tetraptera Maxim (Gentianaceae) endemic to Qinghai-Tibetan Plateau (QTP). A total of 301 individuals from 35 populations of S. tetraptera were analyzed based on two maternally inherited chloroplast fragments (trnL-trnF and trnS-trnG). Phylogeographic analysis was combined with species distribution modeling to detect the genetic variations in S. tetraptera.ResultsThe genetic diversity of S. tetraptera was high, likely due to its wide natural range, high proportion of endemic haplotypes and evolutionary history. Fifty-four haplotypes were identified in S. tetraptera. Only a few haplotypes were widespread (Hap_4, Hap_1, Hap_3), which were dispersed throughout the present geographical range of S. tetraptera, while many haplotypes were confined to single populations. The cpDNA dataset showed that phylogeographic structuring was lacking across the distribution range of S. tetraptera. Analyses of molecular variance showed that most genetic variation was found within populations (70.51%). In addition, the relationships of the haplotypes were almost completely unresolved by phylogenetic reconstruction. Both mismatch distribution analysis and neutrality tests showed a recent expansion across the distribution range of S. tetraptera. The MaxEnt analysis showed that S. tetraptera had a narrow distribution range during the Last Glacial Maximum (LGM) and a wide distribution range during the current time, with predictions into the future showing the distribution range of S. tetraptera expanding.ConclusionOur study implies that the current geographic and genetic distribution of S. tetraptera is likely to have been shaped by Quaternary periods. Multiple microrefugia of S. tetraptera existed during Quaternary glaciations. Rapid intraspecific diversification and hybridization and/or introgression may have played a vital role in shaping the current distribution patterns of S. tetraptera. The distribution range of S. tetraptera appeared to have experienced contraction during the LGM; in the future, when the global climate becomes warmer with rising carbon dioxide levels, the distribution of S. tetraptera will expand.

Vallisneria (Hydrocharitaceae): novel species, taxonomic revisions, and hybridization

Vallisneria is a cosmopolitan genus of aquatic plants comprising 14 species within the family Hydrocharitaceae. Previous research suggests Vallisneria is a more speciose genus than current taxonomy indicates, and there remains contention on the level of species diversity within the genus. In order to address some of these taxonomic issues, this study estimates phylogenetic relationships within the genus using a previously published molecular dataset augmented with previously unsampled species through the use of maximum likelihood analyses for all molecular data partitions (e.g., nrITS, cpDNA, and combined nuclear and cpDNA datasets). Based on our findings, we recommend the resurrection of two Vallisneria species (V. gracilis and V. neotropicalis), and formally recognize and describe a new species (V. jacobsii). Morphological data was shown to be useful for some species delimitation but overall, molecular sequence data provided the best estimates of species identification for cultivated specimens. We also show the presence of naturally occurring putative Vallisneria hybrids within Northern Territory, Australia, and give conclusive evidence that non-native hybrids are being used for a restoration project in Crystal River, Florida.

The molecular phylogenetic position of Harpagocarpus (Polygonaceae) sheds new light on the infrageneric classification of Fagopyrum.

In the context of the molecular phylogeny of Polygonaceae, the phylogenetic positions of most genera and their relationships have been resolved. However, the monotypic genus Harpagocarpus has never been included in any published molecular phylogenetic studies. In the present study, we adopt a two-step approach to confirm the phylogenetic placement of Harpagocarpus using two datasets: (1) a concatenated dataset of three chloroplast DNA (cpDNA) regions (matK, rbcL and trnL-F) for Polygonaceae and (2) a combined cpDNA dataset of five sequences (accD, matK, psbA-trnH, rbcL and trnL-F) for Fagopyrum. Our analyses confirm the previous hypothesis based on morphological, anatomical and palynological investigations that Harpagocarpus is congeneric with Fagopyrum and further reveal that H.snowdenii (≡ F.snowdenii) is sister to the woody buckwheat F.tibeticum. Within Fagopyrum, three highly supported clades were discovered and the first sectional classification was proposed to accommodate them: sect. Fagopyrum comprises the two domesticated common buckwheat (F.esculentum and F.tataricum) and their wild relatives (F.esculentumsubsp.ancestrale, F.homotropicum and F.dibotrys) which are characterised by having large corymbose inflorescences and achenes greatly exceeding the perianth; sect. Tibeticum, including F.snowdenii and F.tibeticum, is characterised by the achene having appurtenances along the ribs, greatly exceeding the perianth and the perianth accrescent in fruit; sect. Urophyllum contains all other species of which the achenes were completely enclosed in the perianth. This study is very helpful to understand the phylogeny of the Fagopyrum and sheds light on the future study of taxonomy, biogeography, diversification and character evolution of the genus.

Trait-linked phylogenetic framework of Paphiopedilum distributed in India revealed species passport trait to prevent unethical trade through in-silico study

• In-silico trait-linked phylogenetic framework of 9 Paphiopedilum species distributed in India based on combined nrDNA and cpDNA ( ITS2 + matK + rbcL ) dataset by MP and Bayesian analysis. • Ancestral trait tracing of 47 characters viz., morphological and chromosomal using Mesquite 3.61. • Sharing of passport traits to public may augment to prevent unethical trade of Paphiopedilum species throughout the distributional range. Paphiopedilum Pfitzer is one of the largest horticulturally utilized genera of slipper orchids. Similar characters of slipper orchids within Paphiopedilum may camouflage identity and mislead a nonprofessional to species substitution. All the species of Paphiopedilum are enlisted in CITES Appendix I and barred for unethical trading from wild sources. An in-silico study on the trait-linked phylogenetic framework of the Paphiopedilum species distributed in India aimed to identify the species passport trait which may prevent unethical trade. The phylogenetic framework was reconstructed using downloaded DNA sequences of ITS2, matK, and rbcL genes from GenBank for 22 slipper orchids of the subfamily Cypripedioideae including 9 Paphiopedilum species of India. Parsimonious and Bayesian interpretations were carried out using PAUP version 4.0a and MrBayes with ancestral trait reconstruction of 47 characters by Mesquite 3.61. The combined DNA ( ITS2 + matK + rbcL ) dataset supported the monophyly of the genus Paphiopedilum with a distinct clade and section Barbata (Krzl.) V.A. Albert & Borge Pett. with a subclade. The monophyly of the conduplicate-leaved genera Paphiopedilum, Phragmipedium, and Mexipedium was congruent to recent taxonomic classifications whereas plicate-leaved Selenipedium and Cypripedium showed polytomy in parsimonious tree. Ancestral reconstruction exhibited basal leaves, conduplicate leaves and deciduous perianth as symplesiomorphic traits. Undulate-revolute, rounded synsepal, ciliate lip; pubescent dorsal sepal, glabrous, glossy lip; coriaceous rough leaves , shortly hirsute peduncle; hairy lip; glandular pubescent peduncle; and brownish dorsal sepal with greenish yellow margin can be considered as passport traits for P. fairrieanum, P. spicerianum, P. venustum, P. charlesworthii, P. druryi and P. hirsutissimum respectively.

Plastid phylogenomics of the Sansevieria Clade of Dracaena (Asparagaceae) resolves a recent radiation

Best known as low maintenance houseplants, sansevierias are a diverse group of flowering plants native to Africa, Madagascar, the Arabian Peninsula, and the Indian subcontinent. Traditionally recognised as a distinct genus, Sansevieria was recently merged with the larger genus Dracaena based on molecular phylogenetic data. Within the Sansevieria Clade of Dracaena, taxonomic uncertainties remain despite attempts to unravel the relationships between the species. To investigate the evolutionary relationships, morphological evolution and biogeographical history in the group, we aim to reconstruct a robust dated phylogenetic hypothesis. Using genome skimming, a chloroplast genome (cpDNA) dataset and a nuclear ribosomal (nrDNA) dataset were generated. The sampling included representatives of all sections and informal groups previously described in Sansevieria based on morphology. Analysis of the cpDNA dataset using a maximum likelihood approach resulted in a well-supported phylogeny. The time-calibrated phylogeny indicated a recent radiation with five main clades emerging in the Pliocene. Two strongly supported clades align with previously defined groups, i.e., Sansevieria section Dracomima, characterised by the Dracomima-type inflorescence, and the Zeylanica informal group, native to the Indian subcontinent. Other previously defined groups were shown to be polyphyletic; a result of convergent evolution of the identifying characters. Switches between flat and cylindrical leaves occurred multiple times in the evolution of the Sansevieria Clade. Similarly, the Cephalantha-type inflorescence has originated multiple times from an ancestor with a Sansevieria-type inflorescence. Analysis of the nrDNA dataset resulted in a phylogenetic hypothesis with low resolution, yet it supported the same two groups confirmed by the cpDNA dataset. This study furthers our understanding of the evolution of the Sansevieria Clade, which will benefit taxonomic and applied research, and aid conservation efforts.

Phylogeny and Biogeography of the Amazonian Pachyptera (Bignonieae, Bignoniaceae)

Abstract—The Amazon houses a large proportion of the overall biodiversity currently found on Earth. Despite that, our knowledge of Amazonian biodiversity is still limited. In this study, we reconstruct the phylogeny of Pachyptera (Bignoniaceae), a genus of neotropical lianas that is centered in the Amazon. We then use this phylogenetic framework to re-evaluate species limits and study the biogeographic history of the genus. We sampled three molecular markers (i.e. ndhF, rpl32-trnL, and PepC) and 51 individuals representing the breadth of morphological variation and geographic distribution of all species recognized in the genus. We used this information to reconstruct phylogenetic relationships among individuals of Pachyptera using Bayesian and maximum likelihood approaches. The resulting molecular phylogeny was used as a basis to test species limits within the P. kerere species complex using a cpDNA coalescent approach (GMYC). GMYC identified five potential species within the P. kerere species complex that were subsequently evaluated in the light of morphology. Morphological data supported the recognition of four of the five potential species suggested by GMYC, all of which were also supported by a multispecies coalescent model in a Bayesian framework. The phylogeny of Pachyptera was time-calibrated and used to reconstruct the biogeographical history of the genus. We identified historically important migration pathways using our comprehensive cpDNA dataset and a Bayesian stochastic search variable selection (BSSVS) framework. Our results indicate that the genus originated in lowland Amazonia during the Middle Eocene, and subsequently occupied Central America and the Andes. Most of the diversification of Pachyptera occurred in the Miocene, a period of intense perturbations in South America.

Sansevieria (Asparagaceae, Nolinoideae) is a herbaceous clade within Dracaena: inference from non-coding plastid and nuclear DNA sequence data

The evolutionary history of the dracaenoid genera Dracaena and Sansevieria (Asparagaceae, Nolinoideae) remains poorly resolved, despite long-recognised issues with their generic boundaries and increased attention paid by both horticulturalists and taxonomists. In this study we aim to: (1) elucidate evolutionary relationships within and between Dracaena and Sansevieria using molecular phylogenetic inference of both nuclear (nDNA) and plastid (cpDNA) markers, (2) examine the infrageneric classifications of each genus, and (3) revise the circumscription of the dracaenoids in light of morphological and phylogenetic evidence. In total, we sampled 21 accessions of Dracaena (ca. 19 species), 27 accessions of Sansevieria (ca. 26 species), and six outgroup taxa. Phylogenetic analyses were based on nucleotide sequences of two non-coding plastid DNA regions, the trnL-F region (trnL intron and trnL-trnF intergenic spacer) and rps16 intron, and the low-copy nuclear region At103. Phylogenetic hypotheses were constructed using maximum parsimony, maximum likelihood, and Bayesian inference. Individual datasets were analysed separately and, after testing for congruence, as combined datasets. We recovered instances of soft incongruence between nDNA and cpDNA datasets in Sansevieria, but general trends in the dracaenoids were congruent, although often poorly supported or resolved. The dracaenoids constitute a strongly supported monophyletic group. Dracaena was resolved as a paraphyletic grade embedded with two clades of Sansevieria, a primary clade comprising most species, and a secondary clade including S. sambiranensis, a distinctive species from Madagascar. The backbone of our phylogeny was only resolved in nDNA analyses, but combined analyses recovered strongly supported species groups. None of the previous infrageneric classifications were supported by our phylogeny, and biogeographic groupings were frequently more significant than morphology. More work is needed to resolve internal relationships in the dracaenoids, but we support a recent proposal to recognise a broadened circumscription of Dracaena that includes Sansevieria. We provide a generic description for the recircumscribed Dracaena and new combinations for several species of Sansevieria in Dracaena.

Nunataks or massif de refuge? A phylogeographic study of Rhodiola crenulata (Crassulaceae) on the world\u2019s highest sky islands

BackgroundQuaternary climatic oscillations had tremendous effects on the current distribution of species. Here, we aim to elucidate the glacial history of Rhodiola crenulata, a perennial herb almost exclusively restricted to rock crevices on mountain peaks, and to test whether the nunatak or massif de refuge hypotheses could explain its distribution pattern.ResultsSix haplotypes and six ribotypes were detected in the cpDNA data set and the ITS data set, respectively. The divergence of R. crenulata and its closest relatives was dated have occurred ca. 0.65 Mya, during the Naynayxungla glaciation on the QTP. Mismatch distribution analysis suggested that the species experienced a range expansion around 0.31 Mya. Populations with high genetic and haplotype diversity were found on the QTP platform as well in the Hengduan Mountains. The ecological niche modeling results showed that there were suitable habitats on both the QTP platform and in the Hengduan Mountains during the LGM.ConclusionOur results support a scenario that both nunataks and the massif de refuge hypotheses could explain the distribution of R. crenulata. We also confirmed that Quaternary climatic oscillations could promote plant speciation in some circumstances. This study adds to a growing body of evidence suggesting that the QTP plant lineages exhibited diverse reactions to the Quaternary climatic oscillations.

Unravelling the phylogeny of the root‐hemiparasitic genus Odontites (tribe Rhinantheae, Orobanchaceae): Evidence for five main lineages

AbstractDespite the recent publication of several phylogenies focused on Rhinantheae, which has been expanded to include three Asian endemic genera, few studies so far have dealt with particular genera within the tribe. Here, we focus on Odontites and related genera because of the high morphological variability of the group and its unclear generic boundaries. Phylogenetic analyses were performed for nrDNA (ITS) and cpDNA (trnK region and rps16 intron) datasets, using Bayesian and Parsimony analyses. Our results cast doubt on the inclusion of Pterygiella and related genera within the Rhinantheae and support the para‐ phyly of Phtheirospermum, making it necessary to propose three new combinations to avoid it. Odontites is recircumscribed to include Bartsiella, Bornmuellerantha, and Macrosyringion, but not Odontitella. Within Odontites, five distinct lineages are identified. These are distinguishable either by morphological synapomorphies or by a combination of several character states. Most of the Odontites species are regarded as monophyletic. In the O. vernus and O. luteus complexes, some taxonomic changes are made to avoid paraphyly, which results in three new combinations.

Historical biogeography of the fern genus Deparia (Athyriaceae) and its relation with polyploidy

The wide geographical distribution of many fern species is related to their high dispersal ability. However, very limited studies surveyed biological traits that could contribute to colonization success after dispersal. In this study, we applied phylogenetic approaches to infer historical biogeography of the fern genus Deparia (Athyriaceae, Eupolypods II). Because polyploids are suggested to have better colonization abilities and are abundant in Deparia, we also examined whether polyploidy could be correlated to long-distance dispersal events and whether polyploidy could play a role in these dispersals/establishment and range expansion. Maximum likelihood and Bayesian phylogenetic reconstructions were based on a four-region combined cpDNA dataset (rps16-matK IGS, trnL-L-F, matK and rbcL; a total of 4252 characters) generated from 50 ingroup (ca. 80% of the species diversity) and 13 outgroup taxa. Using the same sequence alignment and maximum likelihood trees, we carried out molecular dating analyses. The resulting chronogram was used to reconstruct ancestral distribution using the DEC model and ancestral ploidy level using ChromEvol. We found that Deparia originated around 27.7Ma in continental Asia/East Asia. A vicariant speciation might account for the disjunctive distribution of East Asia–northeast North America. There were multiple independent long-distance dispersals to Africa/Madagascar (at least once), Southeast Asia (at least once), south Pacific islands (at least twice), Australia/New Guinea/New Zealand (at least once), and the Hawaiian Islands (at least once). In particular, the long-distance dispersal to the Hawaiian Islands was associated with polyploidization, and the dispersal rate was slightly higher in the polyploids than in diploids. Moreover, we found five species showing recent infraspecific range expansions, all of which took place concurrently with polyploidization. In conclusion, our study provides the first investigation using phylogenetic and biogeographic analyses trying to explore the link between historical biogeography and ploidy evolution in a fern genus and our results imply that polyploids might be better colonizers than diploids.

Phylogeographic study revealed microrefugia for an endemic species on the Qinghai–Tibetan Plateau: Rhodiola chrysanthemifolia (Crassulaceae)

Most phylogeographic studies on the Qinghai–Tibetan Plateau and in adjacent regions have focused on tree or shrub species, or on herbaceous species that mainly inhabit alpine meadows or grasslands. The phylogeography of herbaceous species that inhabit woodlands and shrubberies has been largely neglected. Here we investigate the evolutionary history of a woodland- and shrubbery-inhabited herbaceous species, Rhodiola chrysanthemifolia, which grows in southern Tibet and in the mountains of the Hengduan ecoregion. The cpDNA trnL-F, rpl20-rps12 and nrDNA ITS regions of 183 individuals from 13 populations were sequenced. The ITS dataset revealed a significant phylogeographic structure across the distribution range of R. chrysanthemifolia, while the cpDNA dataset showed no significant structure. Besides, analyses of molecular variance showed that among-population variation was described as 96.27 % of the total variation for ITS marker, much higher than that for cpDNA (63.68 %). Limited seed migration among populations together with inbreeding within populations of R. chsysanthemifolia may result in the different phylogeographic and genetic patterns for ITS and cpDNA markers in this species. A high frequency and an even distribution of private cpDNA haplotypes were discovered throughout the distribution range of R. chrysanthemifolia; ITS genotypes formed three main lineages which showed a geographical distribution pattern. Furthermore, populations with above-average gene diversity were evenly spread across the current distribution range of R. chrysanthemifolia, supporting the existence of microrefugia for this species during Last Glacial Maximum, even earlier glaciations, similar to the pattern of sympatric tree and shrub species of the Juniperus tibetica complex and Hippophae tibetana. Allopatric divergence of populations in isolated microrefugia could be responsible for large number of private cpDNA haplotypes across the current distribution range of R. chrysanthemifolia. The putative factors which drove diversification between R. chrysanthemifolia and R. alsia were also discussed.

Mesoptychia chinensis Bakalin, Vilnet & Xiong sp. nov. (Jungermanniaceae, Marchantiophyta) and comments on the distribution of Mesoptychia south of the boreal zone in Asia

Morphologically unique specimens of Mesoptychia (Lindb.) A.Evans recently collected in Guizhou Province, China were sequenced and analysed using a combined trnL-F+trnG-intron cpDNA dataset from 10 known taxa of Mesoptychia. Using a combination of morphological and molecular data, Mesoptychia chinensis Bakalin, Vilnet & Xiong sp. nov. is described as new to science. Mesoptychia polymorpha subsp. pakistanica Bakalin & Vilnet subsp. nov. is established based on morphological data only. Mesoptychia ussuriensis is newly recorded for China. New molecular data for species delimitation within Mesoptychia distributed in southern and south-east Asia are provided.

Domestication, hybridization, speciation, and the origins of an economically important tree crop of Spondias (Anacardiaceae) from the Brazilian Caatinga dry forest

Domestication can be defined as evolution driven by artificial selection by humans, where individuals possessing desirable characteristics are favored and selectively propagated; over time this process leads to morphological, physiological and genetic changes that distinguish domesticated taxa from their wild ancestors, many times to the point in that the domesticated taxon is regarded as a distinct species. In this paper we address plants of Spondias known by the vernacular name umbu­caja in Northeast Brazil. These plants are found in managed landscapes, but natural populations have not been identified due to widespread cultivation coupled with the clearing of original vegetation. Umbu­caja can be regarded as domesticated because it appears to occur exclusively in cultivation, being actively maintained and propagated by man due to its juicy, delicious fruits. Umbu­caja is referred to as being of hybrid origin in the literature, but this hypothesis remains largely untested experimentally. We carried out a thorough comparative examination of the overall morphology and also a morphometric analysis of leaf and fruit characters of populations of umbu­caja and other Spondias species found in Northeast Brazil. We also reconstructed phylogenies and haplotype networks based on sequences of two non­coding cpDNA regions and the nuclear ETS region in order to ascertain the genetic affinities of umbu­caja. Additionally we estimated the ages of diversification events in Spondias in order to determine when umbu­caja diverged from related species. Although displaying some morphometric intermediacy in the leaves, a number of morphological features readily distinguish umbu­caja from its nearest relatives Spondias tuberosa and S. venulosa. No haplotypes were found to be shared between distinct Spondias species, except in the ETS dataset where umbu­caja and S. tuberosa shared the same haplotype. In the cpDNA dataset, haplotypes of umbu­caja are nearest to haplotypes of S. venulosa, but genetic distances within each taxon are smaller than the genetic distance between the two taxa, suggesting different gene pools for each taxon. There is incongruence in the placement of umbu­caja haplotypes in the cpDNA versus ETS datasets, and also incongruence in the trees recovered from the phylogenetic analyses of both datasets, which is an indication that umbu­caja might have a hybrid origin with S. venulosa and S. tuberosa as its parents. However, umbu­caja was found to have diverged from S. venulosa 3.79 million years ago, indicating that this taxon originated from natural processes. Based on the results of the molecular, morphometric, morphological and time divergence investigations we conclude that umbu­caja should be regarded as distinct lineage that remained undescribed because at present it seems to be only known from cultivation, and also due to its putative hybrid origin. We therefore describe this taxon as Spondias bahiensis sp. nov.

Evolutionary history of Orinus thoroldii (Poaceae), endemic to the western Qinghai-Tibetan Plateau in China

To explore the responses of arid-tolerant alpine plants to Pleistocene climatic oscillations, we examined the evolutionary history of Orinus thoroldii, a grass species endemic to the western Qinghai-Tibetan Plateau (QTP) in China. Three maternally inherited chloroplast DNA (cpDNA) markers (matK, rbcL, and trnH-psbA) and the bi-parentally inherited nuclear ribosomal internal transcribed spacer (nrITS) were sequenced for 243 individuals from 28 populations. In all, seven chloroplast haplotypes (H1–H7) and seven nrITS types (S1–S7) were detected. Whereas two haplotypes were widespread, each of the remaining five was restricted to single populations or shared with only its adjacent population. Phylogenetic analyses of the cpDNA haplotypes revealed two distinct lineages distributed in the eastern and western regions of the western QTP. Our analysis of molecular variance (AMOVA) demonstrated the major partitioning (66.56%) of cpDNA variation between the western and eastern groups. A significant phylogeographical structure was detected (NST = 0.81, GST = 0.72; P < 0.05) based on the cpDNA dataset. The distribution of nrITS types also showed a certain geographical pattern. Whereas types S1 and S5 were widely distributed across the region, the others were exclusively restricted to specific populations. However, the two lineages discerned by the cpDNA sequence variations were not supported by phylogenetic and AMOVA analyses of nrITS variation. Based on documented mutation rates for grasses, we estimated that the two cpDNA lineages of this species diverged at 0.64 Ma during the Pleistocene. This divergence was very consistent with the largest glaciation recorded in the QTP. Long-distance pollen migrations probably blurred the divergence boundary at the nrITS sequence variations. These findings imply that O. thoroldii probably experienced a long-term allopatric divergence plus more recent regional expansions that corresponded to Pleistocene climate changes. Our data also suggest that this grass species survived throughout the Pleistocene glacial stage within the extremely adverse habitats of the QTP.

Generic affiliations of Canthium species placed under Pyrostria group B sensu Bridson (Vanguerieae, Rubiaceae) inferred from morphology and molecular data.

BackgroundPyrostria sensu lato (s.l.) is regarded as one of the polyphyletic group within Vanguerieae formerly comprising of Pyrostria sensu stricto (s.s.), Pyrostria group A and Pyrostria group B delineated by the number of locules and geographical occurrence. Recent molecular phylogenetic studies within the genus have narrowed its circumscription that resulted in the merging of Pyrostria group A and Pyrostria s.s. Although some species of Pyrostria group B were already transferred to Pyrostria s.s. and Psydrax based on morphology, other representatives of the group remain unsettled.ResultsBayesian and parsimony analysis of the combined ITS (nrDNA) and trnL-F (cpDNA) datasets showed a well-supported clade of the whole Vanguerieae containing four Philippine endemic representatives of Pyrostria group B. The placement of Canthium oligophlebium, Canthium obovatifolium and Canthium ramosii within Pyrostria s.s. (PP = 0.99; BS = 85%) is robustly supported likewise the affiliation of C. gynochthodes with Psydrax (PP = 0.94; BS = 85%). Morphological features shared by our species with Pyrostria s.s. and Psydrax further supports our molecular data.ConclusionOur study supports the earlier hypothesis that Canthium oligophlebium, C. obovatifolium and C. ramosii should be placed under Pyrostria s.s. except for C. gynochthodes that grouped with Psydrax. Four new combinations are proposed in this study. The generic affiliations of other species of Pyrostria group B should be reinvestigated towards a more natural classfication in Vanguerieae.Electronic supplementary materialThe online version of this article (doi:10.1186/s40529-014-0065-3) contains supplementary material, which is available to authorized users.

Towards a better understanding of the Taraxacum evolution (Compositae–Cichorieae) on the basis of nrDNA of sexually reproducing species

The genus Taraxacum is characterized by prevailing complex multiple hybridity, frequent polyploidy and widespread agamospermous reproduction, which makes the phylogenetic analysis difficult. On the basis of the previous analysis of the variation of nrDNA in Taraxacum taxa with different ploidy levels and modes of reproduction, to mitigate consequences of the reticulate complexity of the genus, a phylogenetic study of 52 samples of sexually reproducing dandelions of 26 sections (and another 13 agamospermous representatives of other sections known to include sexuals) was carried out. Both sexual and agamospermous samples were analysed using maximum parsimony and neighbour network. Exclusively sexual dandelions were analysed using the same approaches. In spite of the general agreement among various types of analyses, there is a limited overall congruence between results of nrDNA analyses and the established taxonomic system of the genus Taraxacum. The analyses shed light on the relationships among the most primitive groups. A stable clade is formed by representatives of the sections Primigenia, Orientalia, Sonchidium, Piesis and T. cylleneum. Another case of stable relationships is that of the members of the sect. Dioszegia. Relationships between the sects. Erythrosperma and Erythrocarpa were supported, and the relatedness of the members of sect. Australasica was confirmed. Rather unexpectedly, the agamospermous samples of the sect. Oligantha (T. minutilobum) are shown to be closely related with the sect. Macrocornuta. The latter section is generally considered to be close to sect. Ceratoidea (T. koksaghyz) on morphological grounds but this presumption is not corroborated by the results of nrDNA analyses. Analyses of 72 samples of sexual dandelions were also performed using the trnL–trnF region of the chloroplast DNA. The maximum parsimony analysis of this region reveals intraspecific variation in a number of ancestral diploid sexual species, all present in the two main branches of the cladogram. This phenomenon is attributed to the ancient gene flow and possibly to the persistence of ancestral cpDNA polymorphism. The strict consensus cpDNA tree information content and interpretability is quite low. The maximum parsimony analysis of combined nrDNA and cpDNA data sets was also performed with expectably low interpretability of the results.

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.