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Highlights • I suggest a criterion for identifying the root of the tree of life. • The group of organisms with the greatest molecular variability in phylogenetic deep characters represents the root of the tree of life. • Several arguments are advanced for justifying this suggestion. • DPANN archaea and CPR bacteria are suggested as roots of the tree of life. Abstract I suggest –as a criterion for identifying the root of the tree of life – that the group of organisms with the greatest molecular variability in phylogenetic deep characters represents the root of this tree. Indeed, it is expected that in the circumstance of the origin of a given trait several biochemical pathways would have contemporary evolved, for example. The presumed very strong selective pressure acting for the first time on the appearance of the function of that phylogenetically deep trait would have caused its multiple appearance exactly because these traits were originating for the first time. As a result, several pathways would have evolved simultaneously to solve that impelling function. In addition, the evolutionary stage of the progenote would seem that favours per se the formation of these multiple traits – that is to say, performing equivalent or similar function – because it would represent the evolutionary stage in which the origins of all cellular structures occurred. Therefore, it is in this particular evolutionary circumstance that it was – by definition – in the condition that allowed the emergence, for example, of several alternative biochemical pathways to solve the same evolutionary task. Consequently, I here discussed the possibility that the superphylum of DPANN archaea and that of CPR bacteria – especially if considered as a single group of organisms – are/is considered the root of the tree of life, exactly because they would seem to exhibit relatively higher molecular variability in phylogenetically deep characters when compared with other phyla of archaea and bacteria. [ABSTRACT FROM AUTHOR]

Molecular phylogenetic studies of the six currently accepted species in the genus Echinocactus have partially clarified certain aspects of its phylogeny. Most of the studies lack a complete sampling of Echinocactus and are based only in one source of data. Phylogenetic uncertainties in Echinocactus, such as the recognition of Homalocephala as a different genus from Echinocactus, the exclusion of E. grusonii or the affinities of E. polycephalus, are here resolved. Phylogenetic relationships of Echinocactus were reconstructed with a maximum parsimony, a maximum likelihood and a Bayesian approach including 42 morphological characters, four chloroplast markers (atpB-rbcL, trnH-psbA, trnL-trnF and trnK/matK) and two nuclear genes. The utility of these two nuclear regions related to the betalain cycles (DODA and 5GT) are explored and discussed in relation to their potential as phylogenetic markers. Concatenated analyses with morphological and molecular data sets, plus 13 indels (2847 characters and 26 taxa), show general agreement with previous independent phylogenetic proposals but with strong support in order to propose the recognition of a reduced Echinocactus and the recognition of Homalocephala at the generic level. These results recovered a polyphyletic Echinocactus as currently defined. The here-named HEA clade, recovers the species of Homalocephala, Echinocacuts and Astrophytum as a monophyletic group with strong internal support. The Homalocephala (H. texensis, H. parryi and H. polycephala), was recovered as sister to the Echinocactus clade (E. platyacanthus and E. horizonthalonius), plus the Astrophytum clade. Consequently, we propose here to recognise a monophyletic Echinocactus and a monophyletic Homalocephala as two distinct genera with their own molecular and morphological synapomorphies. The evolution of some morphological characters supporting these clades are discussed, the necessary new taxonomic combinations for Homalocephala are proposed and an identification key for the genera, the species and the subspecies of the HEA clade are presented. [ABSTRACT FROM AUTHOR]

The genus Gymnodinium includes many morphologically similar species, but molecular phylogenies show that it is polyphyletic. Eight strains of Gymnodinium impudicum, Gymnodinium dorsalisulcum and a novel Gymnodinium‐like species from Chinese and Malaysian waters and the Mediterranean Sea were established. All of these strains were examined with light microscopy, scanning electron microscopy and transmission electron microscopy. SSU, LSU and internal transcribed spacers rDNA sequences were obtained. A new genus, Wangodinium, was erected to incorporate strains with a loop‐shaped apical structure complex (ASC) comprising two rows of amphiesmal vesicles, here referred to as a new type of ASC. The chloroplasts of Wangodinium sinense are enveloped by two membranes. Pigment analysis shows that peridinin is the main accessory pigment in W. sinense. Wangodinium differs from other genera mainly in its unique ASC, and additionally differs from Gymnodinium in the absence of nuclear chambers, and from Lepidodinium in the absence of Chl b and nuclear chambers. New morphological information was provided for G. dorsalisulcum and G. impudicum, e.g., a short sulcal intrusion in G. dorsalisulcum; nuclear chambers in G. impudicum and G. dorsalisulcum; and a chloroplast enveloped by two membranes in G. impudicum. Molecular phylogeny was inferred using maximum likelihood and Bayesian inference with independent SSU and LSU rDNA sequences. Our results support the classification of Wangodinium within the Gymnodiniales sensu stricto clade and it is close to Lepidodinium. Our results also support the close relationship among G. dorsalisulcum, G. impudicum, and Barrufeta. Further research is needed to assign these Gymnodinium species to Barrufeta or to erect new genera. [ABSTRACT FROM AUTHOR]

Saffron (Crocus sativus L.) is one of the most expensive spices in the world due to its medicinal and aromatic value. However, saffron production is severely affected by the corm rot disease throughout the saffron producing countries. In this study, we report a basidiomycetous latent pathogen of saffron, designated as CSE26, capable of producing phytotoxic compounds. CSE26 is a highly odorous basidiomycete with monomitic hyphal system. Molecular phylogeny of ITS and 28S ribosomal gene sequence of CSE26 assigned it as Porostereum spadiceum. It was found to produce corm rot in C. sativus under in vivo and field conditions, with a disease severity index of 0.7 and 0.5, respectively. CSE26 was found to produce chlorinated aromatic compounds (CAMs) having phytotoxic activity against Arabidopsis plants. Therefore, these compounds may be acting as pathogenic determinants of CSE26. However, there is a need to study the level of production of these CAMs by this fungus in the natural environment and their effects on plant health. [ABSTRACT FROM AUTHOR]

In this study, we performed sequence, physicochemical, phylogenetic, and comparative 3D (three-dimensional) analyses of RuBisCO large subunit proteins of the Morus species using various bioinformatics tools. The sequence lengths of the RuBisCO proteins varied between 140 and 475 amino acids with molecular weights (MW) ranging from 15463.40 to 52667.95 Da. The most acidic protein sequences were in M. australis, M. rotundiloba, M. serrata, and M. cathayana (pI=4.77). The extinction coefficients of the proteins at 280 nm ranged from 21430 to 69830 M-1 cm-1, the instability index (II) values ranged from 26.06 to 42.17, and the GRAVY values ranged from -0.355 to -0.215. The most abundant amino acid of RuBisCO proteins was Gly (9.5%) while the least abundant ones were Cys and Trp (1.5%). Based on the phylogenetic analysis, the tree constructed using RuBisCO proteins is composed of three main clades. A RAMPAGE analysis revealed that 96.1% - 98.5% of residues were located in the favored region in RuBisCO proteins. To predict the three dimensional (3D) structures of the RuBisCO proteins PyMOL was used. The highest number of Gly residues was detected in M.mongolica, M. indica, M.notabilis, M. alba var. atropurpurea and M. alba var. multicaulis, while the least Gly residues were detected in M. australis, M.rotundiloba, M. serrata and M.cathayana. The results of our study provide insights into fundamental characteristic of RuBisCO proteins in Morus species. [ABSTRACT FROM AUTHOR]

Gliadins, as the major components of wheat storage proteins, determine the extensibility properties of dough and have important effects on flour processing quality. Wheat related species carries potential storage protein gene resources for quality improvement. In this study, we isolated and characterized the first complete ω-gliadin gene Omega-AS from Aegilops speltoides L. (2n = 2x = 14, SS) by allelic-specific PCR and investigated its phylogenetic relationships among Triticum and Aegilops species. Molecular structure showed that Omega-AS gene consisted of 1122 bp encoding 373 amino acid residues with deduced molecular mass 41379.21 Da. Omega-AS gene was exceptionally rich in prolines and glutamines with fewer methionine and no cysteine. Sequence characterization and epitope analysis showed that three epitopes QQPIPVQPQQ, TQPQQPTPIQ and IQPQQPFPQQ were absent in Omega-AS gene encoded protein, indicating its potential value for wheat quality improvement with less toxic, or no toxic peptides . Phylogenetic analysis revealed that Omega-AS was closely related to gliadin genes of wheat and related species and its divergence from bread wheat was more recently (less than 1.243 MYA). Heterologous expression showed that Omega-AS gene could successfully express with a high level in E. coli under the control of T7 promoter. The transcription expression pattern of Omega-AS gene during grain development detected by qRT-PCR revealed that the highest expression level occurred at 17 days post anthesis. [ABSTRACT FROM AUTHOR]

Daedaleopsis spp., a lignicolous fungus causes of white rot on wild cherry and other broadleaved species and makes economic losses in Serbian forestry. The paper presents results of two morphologically distinct fungi Daedaleopsis confragosa and Daedaleopsis tricolor isolated from native populations of wild cherry (Prunus avium L.) found in the sites of Protected Forests of Serbia. Morphological appearance of D. tricolor was found more abundant in comparison to D. confragosa species. Samples from Serbia were analysed using morphometric and molecular tools and compared with isolates from United Kingdom and published sequences from Sweden, Austria, Hungary, Germany, Canada, France, USA and Czech Republic to give the taxonomic insight and their genetic relatedness using fungal barcoding region ITS rDNA. Results from BLAST search confirmed morphology of the isolates to their taxonomic affiliation as D. confragosa while sequence analysis showed mutations at several polymorphic positions that indicates genetic divergence to D. tricolor. Phylogenetic analysis presents narrow genetic relations of Serbian isolates with the one from United Kingdom while distinctness from other countries investigated specimens. Future work needs variable regions for both species to be amplified in order to evaluate species boundaries or employing NGS technologies in more detailed sequence analyses. [ABSTRACT FROM AUTHOR]

The predominantly Asian tribe Miliuseae (Annonaceae) includes over 37 Neotropical species that are mainly distributed across Mesoamerica, from southern Mexico to northern Colombia. The tremendous ecological and morphological diversity of this clade, including ramiflory, cauliflory, flagelliflory, and clonality, suggests adaptive radiation. Despite the spectacular phenotypic divergence of this clade, little is known about its phylogenetic and evolutionary history. In this study we used a nuclear DNA marker and seven chloroplast markers, and maximum parsimony, maximum likelihood and Bayesian inference methods to reconstruct a comprehensive time-calibrated phylogeny of tribe Miliuseae, especially focusing on the Desmopsis-Stenanona clade. We also perform ancestral area reconstructions to infer the biogeographic history of this group. Finally, we use ecological niche modeling, lineage distribution models, and niche overlap tests to assess whether geographic isolation and ecological specialization influenced the diversification of lineages within this clade. We reconstructed a monophyletic Miliuseae that is divided into two strongly supported clades: (i) a Sapranthus - Tridimeris clade and (ii) a Desmopsis - Stenanona clade. The colonization of the Neotropics and subsequent diversification of Neotropical Miliuseae seems to have been associated with the expansion of the boreotropical forests during the late Eocene and their subsequent fragmentation and southern displacement. Further speciation within Neotropical Miliuseae out of the Maya block seems to have occurred during the last 15 million years. Lastly, the geographic structuring of major lineages of the Desmopsis - Stenanona clade seems to have followed a climatic gradient, supporting the hypothesis that morphological differentiation between closely related species resulted from both long-term isolation between geographic ranges and adaptation to environmental conditions. [ABSTRACT FROM AUTHOR]

Inferring interfamilial relationships within the eudicot order Ericales has remained one of the more recalcitrant problems in angiosperm phylogenetics, likely due to a rapid, ancient radiation. As a result, no comprehensive time-calibrated tree or biogeographical analysis of the order has been published. Here, we elucidate phylogenetic relationships within the order and then conduct time-dependent biogeographical and diversification analyses by using a taxon and locus-rich supermatrix approach on one-third of the extant species diversity calibrated with 23 macrofossils and two secondary calibration points. Our results corroborate previous studies and also suggest several new but poorly supported relationships. Newly suggested relationships are: (1) holoparasitic Mitrastemonaceae is sister to Lecythidaceae, (2) the clade formed by Mitrastemonaceae + Lecythidaceae is sister to Ericales excluding balsaminoids, (3) Theaceae is sister to the styracoids + sarracenioids + ericoids, and (4) subfamilial relationships with Ericaceae suggest that Arbutoideae is sister to Monotropoideae and Pyroloideae is sister to all subfamilies excluding Arbutoideae, Enkianthoideae, and Monotropoideae. Our results indicate Ericales began to diversify 110 Mya, within Indo-Malaysia and the Neotropics, with exchange between the two areas and expansion out of Indo-Malaysia becoming an important area in shaping the extant diversity of many families. Rapid cladogenesis occurred along the backbone of the order between 104 and 106 Mya. Jump dispersal is important within the order in the last 30 My, but vicariance is the most important cladogenetic driver of disjunctions at deeper levels of the phylogeny. We detect between 69 and 81 shifts in speciation rate throughout the order, the vast majority of which occurred within the last 30 My. We propose that range shifting may be responsible for older shifts in speciation rate, but more recent shifts may be better explained by morphological innovation. [ABSTRACT FROM AUTHOR]

Premise of research. Odontites is an herbaceous genus composed of 27 species, mostly distributed around the Mediterranean Basin. As a first step toward studying species diversification within this genus, our goals were to (i) test previous hypotheses about phylogenetic relationships among species; (ii) assess whether the closely related genera Bartsiella, Bornmuellerantha, Macrosyringion, and Odontitella should be included in Odontites; and (iii) detect potential events of reticulate evolution. Methodology. We estimated phylogenetic relationships based on nuclear (ITS and ETS) and chloroplast (psbA-trnH, trnC-ycf6, and trnL-trnF) DNA regions. Our sampling included 184 individuals representing 25 out of the 27 species of Odontites. We also counted chromosomes in five species and measured nuclear genome sizes in 139 individuals of 21 species. Pivotal results. We showed that Bartsiella and Bornmuellerantha should be returned to Odontites, while Odontitella was confirmed as distinct. Macrosyringion requires further investigations. Several phylogenetic incongruences were identified, suggesting two cases of hybrid speciation (in O. maroccanus and O. violaceus) and several introgression events. These events were very diverse in terms of number of individuals involved, species co-occurrence, direction of introgression, and incidence of genome doubling. We obtained new chromosome numbers for O. hispidulus (2np4xp40) and O. powellii (2np2xp20), and no relation between nuclear genome size and chromosome number was found. Conclusions. We inferred hybrid speciation and various introgression events, and polyploidy was also detected. Odontites appears as an interesting genus to study species diversification, providing a group of closely related species that display, e.g., morphological, ecological, or phenological character variation; cases of study at different temporal stages in the diversification process; and several contact zones between species. [ABSTRACT FROM AUTHOR]

Premise of research. Campyloneurum is entirely Neotropical with about 60 generally accepted species. Although a prominent, mostly epiphytic genus in Neotropical forests, no research has been done previously on its phylogeny or character evolution.Methodology. We obtained sequence data from four plastid markers (rbcL, trnG-trnR, trnL-trnF, and rps4-trnS) of 44 species of Campyloneurum, or 73% of the species in the genus. The sequence data were analyzed using Bayesian and maximum likelihood methods. Herbarium specimens were examined to code morphological characters, and spores were imaged with the scanning electron microscope. Growth form and five morphological character states were optimized on the trees using parsimony.Pivotal results. We confirm most previous studies that Campyloneurum forms a clade with Microgramma and Niphidium. The three genera are generally characterized by simple entire leaves, areolate venation, and included veins within the areoles. Within Campyloneurum, seven main clades were recovered, some of which were defined by distinctive geography or morphological characters such as pruinose rhizomes, long-creeping rhizomes, or one-pinnate leaves. The spores were uniform and did not provide any grouping information. The genus has its highest endemism and diversity in the Andes, with the mountains of Costa Rica and Panama being a secondary center. A map is given showing the estimated species richness and percent endemism of Campyloneurum in different geographical regions of the Neotropics.Conclusions. This study presents the first phylogenetic analysis of Campyloneurum. The genus forms a clade with Microgramma and Niphidium. Within the genus, seven main clades were recognized, some of which are supported by distinctive morphological synapomorphies. A clade of five species is endemic to southeastern Brazil. Our tree suggests that many undescribed species occur in the genus, indicating the need for more taxonomic studies at the species level. [ABSTRACT FROM AUTHOR]

During dismantling and relocation of the Takamatsuzuka Tumulus stone chamber, many Cladophialophora and chaetothyrialean black fungi, such as Exophiala and Phialophora , were isolated from samples taken from the joints between the stone walls. However, inside the stone chamber of the Kitora Tumulus, after intermittent UV irradiation in 2009, these black fungi were also isolated from samples taken from the stone walls. Molecular phylogenetic analyses based on only nrLSU and the concatenated (nrLSU D1/D2 + ITS) sequences revealed that the 35 Takamatsuzuka and Kitora Tumuli isolates of Cladophialophora and the chaetothyrialean black fungi were divergent. Two new species of Cladophialophora are described herein: C. tumulicola from the viscous gels and various substrates on the stone walls of the Takamatsuzuka and Kitora Tumuli and C. tumbae from black substances on the plastic cover over the “thief hole,” soil and plaster pieces between the stone walls, and the exterior of the Takamatsuzuka Tumulus chamber. Also, molecular phylogenetic placements for the remaining eight Takamatsuzuka and Kitora Tumuli isolates of chaetothyrialean black fungi have been determined or suggested. [ABSTRACT FROM AUTHOR]

A new ginger species, Curcuma cotuana (subg. Ecomatae), from Tây Giang District, Quảng Nam Province, central Vietnam, is reported here. A detailed description, colour plates, and comparison with the morphologically closest allies are given, together with preliminary conservation assessments and notes on its uses by local people. [ABSTRACT FROM AUTHOR]

The two cultivated Canavalia (Adanson, 1763) species, Canavalia gladiata (N. J. von Jacquin, 1788) A. P. de Candolle, 1825 and Canavalia ensiformis (Linnaeus, 1753) A. P. de Candolle, 1825 are closely related based on morphological and molecular phylogenetic data. However, the similarities and differences in genome organization between them have not been evaluated at molecular cytogenetic level. Here, detailed karyotypes of both species were constructed using combined PI and DAPI (CPD) staining, rDNA-FISH and self-genomic in situ hybridization (sGISH). For further comparison, comparative genomic in situ hybridization (cGISH) and sequence analysis of 5S rDNA were applied. Their chromosomes were accurately identified by sGISH and rDNA-FISH signals. Both species had the karyotype formula 2n = 22 = 18m + 4m-SAT, but the karyotype of C. ensiformis was shorter and more asymmetric than that of C. gladiata. They displayed similar CPD bands at all 45S rDNA sites and centromeres. C. gladiata had ten centromeric 5S rDNA loci and two SC (secondary constriction)-associated 45S rDNA loci. C. ensiformis had nine centromeric and one interstitial 5S loci, two SC-associated and one proximal 45S loci. Their sGISH signal patterns displayed both basic similarities and distinct differences. Reciprocal cGISH generated prominent signals in all pericentromeric regions and 45S sites. There was lower level of sequence identity of the non-transcribed spacer between their 5S rDNA repeats. These data confirmed the evolutionary closeness between C. gladiata and C. ensiformis and demonstrated obvious differentiation between their genomes, and supported the opinion that C. ensiformis is more advanced in evolution than C. gladiata. [ABSTRACT FROM AUTHOR]

The Andean mountains of South America are the most species-rich biodiversity hotspot worldwide with c. 15% of the world's plant species, in only 1% of the world's land surface. Orchids are a key element of the Andean flora, and one of the most prominent components of the Neotropical epiphyte diversity, yet very little is known about their origin and diversification., We address this knowledge gap by inferring the biogeographical history and diversification dynamics of the two largest Neotropical orchid groups (Cymbidieae and Pleurothallidinae), using two unparalleled, densely sampled orchid phylogenies (including more than 400 newly generated DNA sequences), comparative phylogenetic methods, geological and biological datasets., We find that the majority of Andean orchid lineages only originated in the last 20-15 million yr. Andean lineages are derived from lowland Amazonian ancestors, with additional contributions from Central America and the Antilles. Species diversification is correlated with Andean orogeny, and multiple migrations and recolonizations across the Andes indicate that mountains do not constrain orchid dispersal over long timescales., Our study sheds new light on the timing and geography of a major Neotropical diversification, and suggests that mountain uplift promotes species diversification across all elevational zones. [ABSTRACT FROM AUTHOR]

A new name, Topea H. A. Keller, is proposed for the genus Aenigma H. A. Keller (Apocynaceae) because there is a preexisting phonetic homonym. In addition, based on molecular phylogenetic studies, the new, monogeneric subtribe Topeinae H. A. Keller & Liede, endemic to the southern cone of South America, is here described within the tribe Asclepiadeae. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis based on 18S nuclear ribosomal DNA and four plastid markers (atpB, matK, rbcL and trnLF) strongly supports the position of a new genus in Euphorbiaceae tribe Epiprineae (subfamily Acalyphoideae). Tsaiodendron dioicum gen. nov., sp. nov. is described and illustrated here as a new genus and species from Yunnan province, south-western China. The phylogenetic position of the new taxon is also supported by morphological and palynological evidence. Tsaiodendron is a distinct lineage sister to Cladogynos in tribe Epiprineae and is easily distinguished from related members of the tribe by the sexual system, inflorescence arrangement and presence of disc glands in the pistillate flower. Molecular divergence dating analysis based on matK, rbcL and trnL-F sequences suggests that Tsaiodendron originated in the late Miocene 10.42 Mya (95% HPD: 5.23--18.88 Mya). The origin of Tsaiodendron may be correlated with the Red River incision from south-western China. Tribe Epiprineae are shown to be monophyletic and phylogenetic relationships and evolutionary trends in the sexual system are also discussed based on our phylogenetic results. [ABSTRACT FROM AUTHOR]

Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence dates of pines based on a large number of fossils (21) evenly distributed across all major clades, in combination with applying both node and tip dating methods. Results: We present a range of molecular phylogenetic trees of Pinus generated within a Bayesian framework. We find the origin of crown Pinus is likely up to 30 Myr older (Early Cretaceous) than inferred in most previous studies (Late Cretaceous) and propose generally older divergence times for major clades within Pinus than previously thought. Our age estimates vary significantly between the different dating approaches, but the results generally agree on older divergence times. We present a revised list of 21 fossils that are suitable to use in dating or comparative analyses of pines. Conclusions: Reliable estimates of divergence times in pines are essential if we are to link diversification processes and functional adaptation of this genus to geological events or to changing climates. In addition to older divergence times in Pinus, our results also indicate that node age estimates in pines depend on dating approaches and the specific fossil sets used, reflecting inherent differences in various dating approaches. The sets of dated phylogenetic trees of pines presented here provide a way to account for uncertainties in age estimations when applying comparative phylogenetic methods. [ABSTRACT FROM AUTHOR]

The development of functional chloroplasts, which is assisted by a series of nuclear-encoded auxiliary protein factors, is essential for plant autotrophic growth and development. To understand the molecular mechanisms underlying chloroplast development, we isolated and characterized a pigment-defective mutant, pdm2, and its corresponding variegated RNA interference (RNAi) lines in Arabidopsis. Sequence analysis revealed that PDM2 encodes a pentatricopeptide repeat protein that belongs to the P subgroup. Confocal microscopic analysis and immunoblotting of the chloroplast protein fraction showed that PDM2 was located in the stroma. In RNAi plants, protein-related photosynthesis was severely compromised. Furthermore, analysis of the transcript profile of chloroplast genes revealed that plastid-encoded polymerase-dependent transcript levels were markedly reduced, while nuclearencoded polymerase-dependent transcript levels were increased, in RNAi plants. In addition, PDM2 affects plastid RNA editing efficiency in most editing sites, apparently by directly interacting with multiple organellar RNA editing factor 2 (MORF2) and MORF9. Thus, our results demonstrate that PDM2 is probably involved in the regulation of plastid gene expression required for normal chloroplast development. [ABSTRACT FROM AUTHOR]

Plant disjunctions between the temperate regions of the northern and southern hemisphere, commonly called amphitropical or bipolar disjunctions, have been discussed by numerous authors but very little attention has been paid to the occurrence of such disjunctive ranges in the complex thalloids (Marchantiidae). A perusal of the literature revealed 20 species of Marchantiidae with amphitropical ranges, in eight genera (Asterella,Clevea,Corsinia,Cryptomitrium,Oxymitra,Riccia,RiellaandSphaerocarpos). These amphitropical species are distributed in subtropical and Mediterranean regions of the northern and southern hemisphere but not, or rarely, in the tropics. The majority are disjunctive between North America and southern South America and between Eurasia and South Africa. Long-distance dispersal of spores via birds is considered the most plausible natural cause of these amphitropical ranges. About two-third of the species have bisexual spores, which should be advantageous to long-distance dispersal. Extinction due to past climatic fluctuations may also have played a role but fossil evidence is lacking. A few species have attained their amphitropical range by human-mediated introduction:Riccia warnstorfiiLimpr. andSphaerocarpos texanusAustin were presumably introduced in the southern hemisphere whereasS. stipitatusBisch.exLindenb. from Central Chile and South Africa is adventive in the northern hemisphere. The amphitropical ranges exhibited by a number of complex thalloid species are solely based on morphological, floristic and ecological evidence and have not been tested by molecular analysis. Careful comparisons of the northern and southern populations based on an integrated molecular-phylogenetic, morphological-anatomical and chemical approach should be carried out. [ABSTRACT FROM AUTHOR]

The present study provides evidence for taxonomic delimitation of Digitaria sect. Trichachne based on morphological data (micro- and macromorphology) and molecular data. A phylogenetic analysis was performed using 121 morphological characters and ITS sequences of 22 species and one variety of Digitaria plus three outgroups. In all topologies (based on morphological, molecular, and combined data) Digitaria sect. Trichophorae was non-monophyletic and nested within D. sect. Trichachne. Digitaria sect. Trichophorae is thus synonymized under D. sect. Trichachne and the circumscription of D. sect. Trichachne is emended. Diagnostic morphological characters related to spikelet structure are described and documented with SEM. A key to taxa belonging to D. sect. Trichachne is provided, as well as a synopsis including synonymy, iconography, geographical distribution, and ecology. The neotype of Trichachne sacchariflora Nees is herein designated. Complete illustrations of Digitaria eggersii, D. hitchcockii, and D. patens are provided. The phylogenetic placement of the Australian species D. brownii differed among trees resulting from different data sets, thus it is provisionally not included in D. sect. Trichachne in spite of its morphological similarity. Furthermore, Megaloprotachne albescens is formally transferred to Digitaria, as Digitaria albescens. [ABSTRACT FROM AUTHOR]

Background and Aims The patterns of evolutionary assembly in the Sino-Japanese floristic region (SJFR) remain largely unknown due to a lack of integrative multidimensional studies throughout the region. To address this issue, we elucidated the evolutionary history of Cardiocrinum (Liliaceae), a genus containing four taxa distributed across the SJFR. Methods Fifty-four populations were sampled throughout the geographical range of Cardiocrinum to assess genetic structure, analyse phylogenetic relationships and reconstruct ancestral area based on six chloroplast DNA (cpDNA) fragments and three low copy nuclear genes (LCNG). Ecological niche modelling was used to examine the potential range shifts of Cardiocrinum in response to climatic change. Key Results The molecular data showed high genetic similarity in the cpDNA (98·37 %) and LCNG (94·53 %) sequences. The biogeographical analyses revealed that the ancestor of Cardiocrinum diversified during the late Miocene (approx. 7·32 Mya) in Central China. The ancestor of the C. giganteum lineage dispersed westward to the Himalayas and south-west China with the split between C. giganteum and C. giganteum var. yunnanense occurring around 4·11 Mya consistent with the period of orogeny of the Hengduan Mountains. Some populations of the C. cathayanum lineage dispersed eastward to south Japan via the land bridge approx. 4·97 Mya, providing opportunities for allopatric speciation of C. cordatum. The predicted suitable habitats of Cardiocrinum have become smaller and more fragmented since the Last Glacial Maximum. Conclusions Our study provides evidence of a biogeographical pattern of dispersal from Central China to the Himalayas in the west and Japan in the east for genera distributed across the SJFR, and highlights that the orogeny of the Hengduan Mountains and fluctuations of the sea level of the East China Sea played important roles in promoting species divergence. [ABSTRACT FROM AUTHOR]

Limosella is a small aquatic genus of Scrophulariaceae of twelve species, of which one is distributed in northern circumpolar regions, two in southern circumpolar regions, two in the Americas, one endemic to Australia, and six in tropical or southern Africa or both. The Australasian L. curdieana has always been considered distinct but its close phylogenetic relationships have never been inferred. Here, we investigated the following alternative phylogenetic hypotheses based on comparative leaf morphology and habitat preferences or floral morphology: (1) L. curdieana is sister to the African L. grandiflora; or (2) it is closely related to a group of other African species and the northern circumpolar L. aquatica. We tested these hypotheses in a phylogenetic framework using DNA sequence data from four plastid DNA regions and the nuclear ITS region. These were analyzed using maximum parsimony and Bayesian inference. We obtained moderately resolved, partially conflicting phylogenies, supporting that accessions of L. grandiflora form the sister group to the rest of the genus and that L. curdieana groups with the African taxa, L. africana and L. major, and L. aquatica. Thus, the molecular evidence supports the second hypothesis. A biogeographic analysis suggests an out-of-southern Africa scenario and several dispersal events in the Southern Hemisphere. Past dispersal from southern Africa to Australasia is suggested, yet it cannot be excluded that a route via tropical Africa and temperate Asia has existed. [ABSTRACT FROM AUTHOR]

The Labrador teas are a group of nearly circumboreal shrubs or sub-shrubs inhabiting damp habitats. The 4-7 currently recognized species are classified within Rhododendron subg. Rhododendron section Rhododendron subsect. Ledum. In floral characters, these species are extremely similar. In vegetative characters, species limits in the Labrador teas have been difficult to determine because many of the traditionally used morphological characters vary continually across the geographic range. This study investigated evolutionary history and preliminary consideration of some species boundaries in the Labrador teas using DNA sequence data from five molecular markers to generate a preliminary phylogeny of R. subsect. Ledum. Data were analyzed using Maximum Parsimony, Maximum Likelihood and Bayesian methods. The nuclear data indicate a monophyletic subsect. Ledum, but chloroplast data indicate that the North American taxa have an evolutionary history separate from the European and Asian taxa, suggesting that one or both lineages of subsect. Ledum may be of hybrid origin. Additionally, our analyses suggest that taxa combined in recent treatments (i.e. Rhododendron tomentosum) represent separate lineages and should be recognized as distinct instead of included within more broadly defined species, however our current level of sampling cannot completely resolve this issue. This study lays the groundwork for future phylogenetic studies within subsect. Ledum, illustrating the need to sample more intensively across taxa in order to capture what appears to be a complex genetic and biogeographic history. [ABSTRACT FROM AUTHOR]

Lamont et al. (2016) concluded that the Australian sclerophyllous genus Hakea (Proteaceae) arose 18 million years ago in the South West of Western Australia (SWA) and dispersed 18 times to eastern (EA) and central Australia (CA) only 12 million years ago (mid-Miocene). Their explanation of the biogeographic history of Hakea was based on the following: accepting a fully resolved molecular phylogenetic tree, although ~40% of nodes had posterior probability values below 0.95; using all nodes including geographically paralogous nodes to determine ancestral area probabilities; and applying a strict clock to estimate clade divergence times. Our re-analyses of the same dataset using a relaxed clock model pushes the age of Hakea to 32.4 (21.8-43.7) million years ago relative to its nearest outgroups, and the age of the divergence of two major clades (A and B) to 24.7 (17.2-33.7) million years ago. Calibration based on a new finding of Late Cretaceous fossil Banksia pushes these dates to 48.0 (24.3-75.2) million years ago and 36.6 (18.5-55.4) million years ago respectively. We confirm that each of the two main clades includes lineages in SWA, CA and EA. At the basal node of Clade A, two eastern Australian species form the sister group to three SWA scrub–heath–Eremaean species. These two groups together are sister to a large, mostly unresolved clade of SWA, CA and EA taxa. Similarly, at the base of Clade B is a polytomy of lineages from the SWA, CA and EA, with no resolution of area relationships. There is no evidence of a centre of origin and diversification of the genus is older than the mid-Miocene, being at least Oligocene, and probably older, although calibration points for molecular dating are too far removed from the ingroup to provide any great confidence in the methodology. Consideration should be given to the possibility of vicariance of multiple, widespread ancestral lineages as an explanation for lineages now disjunct between EA and SWA. [ABSTRACT FROM AUTHOR]

Cyst echinococcosis caused by the matacestodal larvae of Echinococcus granulosus ( Eg), is a chronic, worldwide, and severe zoonotic parasitosis. The treatment of cyst echinococcosis is still difficult since surgery cannot fit the needs of all patients, and drugs can lead to serious adverse events as well as resistance. The screen of target proteins interacted with new anti-hydatidosis drugs is urgently needed to meet the prevailing challenges. Here, we analyzed the sequences and structure properties, and constructed a phylogenetic tree by bioinformatics methods. The MIP family signature and Protein kinase C phosphorylation sites were predicted in all nine EgAQPs. α-helix and random coil were the main secondary structures of EgAQPs. The numbers of transmembrane regions were three to six, which indicated that EgAQPs contained multiple hydrophobic regions. A neighbor-joining tree indicated that EgAQPs were divided into two branches, seven EgAQPs formed a clade with AQP1 from human, a 'strict' aquaporins, other two EgAQPs formed a clade with AQP9 from human, an aquaglyceroporins. Unfortunately, homology modeling of EgAQPs was aborted. These results provide a foundation for understanding and researches of the biological function of E. granulosus. [ABSTRACT FROM AUTHOR]

The species-rich and diverse genus Pimpinella is mainly distributed in Europe and Asia; a few species occur in Africa. Yet, the Javanian Pimpinella, P. pruatjan, which has been used as an aphrodisiac in Indonesian traditional medicine, was studied for the first time in the context of chemical composition, as well as phylogeny analysis and antimicrobial activity. We examined the chemical composition of the essential oil (EO) from aerial parts of P. pruatjan by gas liquid chromatography-mass spectrometry (GLC-MS). The main component of EO was (Z)- γ -bisabolene. Several oxygenated monoterpenes, oxygenated sesquiterpenes, and sesquiterpenes were also detected. The genetic relationship of Pimpinella pruatjan Molk. to other Pimpinella species was reconstructed using nucleotide sequences of the nuclear DNA marker ITS (Internal Transcribed Spacer). P. pruatjan clusters as a sister group to the African Pimpinella species. The EO did not exhibit an apparent antimicrobial activity. [ABSTRACT FROM AUTHOR]

The tank-epiphytic clade of berry-fruited bromeliads, also known as the Core Bromelioideae, represents a remarkable event of adaptive radiation within the Bromeliaceae; however, the details of this radiation have been difficult to study because this lineage is plagued with generic delimitation problems. In this study, we used a phylogenetic approach to investigate a well supported, albeit poorly understood, lineage nested within the Core Bromelioideae, here called the “ Ronnbergia Alliance”. In order to assess the monophyly and phylogenetic relationships of this group, we used three plastid and three nuclear DNA sequence markers combined with a broad sampling across three taxonomic groups and allied species of Aechmea expected to comprise the Ronnbergia Alliance. We combined the datasets to produce a well-supported and resolved phylogenetic hypothesis. Our main results indicated that the Ronnbergia Alliance was a well-supported monophyletic group, sister to the remaining Core Bromelioideae, and it was composed by species of the polyphyletic genera Aechmea , Hohenbergia and Ronnbergia. We identified two major internal lineages with high geographic structure within the Ronnbergia Alliance. The first of these lineages, called the Pacific Clade, contained species of Aechmea and Ronnbergia that occur exclusively from southern Central America to northwestern South America. The second clade, called the Atlantic Clade, contained species of Aechmea , Hohenbergia and Ronnbergia mostly limited to the Atlantic Forest and the Caribbean. We also explored the diagnostic and evolutionary importance of 13 selected characters using ancestral character reconstructions on the phylogenetic hypothesis. We found that the combination of tubular corollas apically spreading and unappendaged ovules had diagnostic value for the Ronnbergia Alliance, whereas flower size, length of the corolla tube, and petal pigmentation and apex were important characters to differentiate the Pacific and Atlantic clades. This study opens new perspectives for future taxonomic reorganizations and provides a framework for evolutionary and biogeographic studies. [ABSTRACT FROM AUTHOR]

Positive selection is known to drive the evolution of genes involved in evolutionary arms races, but what role does it play in the evolution of genes involved in developmental processes? We used the single-celled epidermal trichomes of Brassicaceae as a model to uncover the molecular evolutionary processes that contributed to the transition from dendritic trichomes, as seen in most species of Brassicaceae, to the distinctive stellate trichomes of the genus Physaria . We explored the role of positive selection on the evolution of BRANCHLESS TRICHOME ( BLT ), a candidate gene for changes in trichome branching pattern. Maximum likelihood models of codon evolution point to a shift in selective pressure affecting the evolution of BLT across the entire Physaria clade, and we found strong evidence that positive selection has acted on a subset of Physaria BLT codons. Almost all of the 10 codon sites with the highest probability of having evolved under positive selection are clustered in a predicted coiled-coil domain, pointing to changes in protein–protein interactions. Thus, our findings suggest that selection acted on BLT to modify its interactions with other proteins. The fact that positive selection occurred throughout the radiation of Physaria could reflect selection to stabilize development in response to an abrupt switch from the dendritic form to the stellate form, divergent selection for diversification of the stellate form, or both. These results point to the need for evolutionary developmental studies of BLT and its interacting proteins in Physaria . [ABSTRACT FROM AUTHOR]

Discerning relationships among species evolved by reticulate and/or polyploid evolution is not an easy task, although it is widely discussed. The economically important genus Curcuma (ca. 120 spp.; Zingiberaceae), broadly distributed in tropical SE Asia, is a particularly interesting example of a group of palaeopolyploid origin whose evolution is driven mainly by hybridization and polyploidization. Although a phylogeny and a new infrageneric classification of Curcuma , based on commonly used molecular markers (ITS and cpDNA), have recently been proposed, significant evolutionary questions remain unresolved. We applied a multilocus approach and a combination of modern analytical methods to this genus to distinguish causes of gene tree incongruence and to identify hybrids and their parental species. Five independent regions of nuclear DNA ( DCS , GAPDH , GLOBOSA3 , LEAFY, ITS) and four non-coding cpDNA regions ( trn L- trn F, trn T- trn L, psb A- trn H and mat K), analysed as a single locus, were employed to construct a species tree and hybrid species trees using * BEAST and STEM-hy. Detection of hybridogenous species in the dataset was also conducted using the posterior predictive checking approach as implemented in JML. The resulting species tree outlines the relationships among major evolutionary lineages within Curcuma , which were previously unresolved or which conflicted depending upon whether they were based on ITS or cpDNA markers. Moreover, by using the additional markers in tests of plausible topologies of hybrid species trees for C. vamana, C. candida , C. roscoeana and C. myanmarensis suggested by previous molecular and morphological evidence, we found strong evidence that all the species except C. candida are of subgeneric hybrid origin. [ABSTRACT FROM AUTHOR]

Several attempts have been made to generate complete species-level phylogenies for large clades, enabling comprehensive analyses of ecological or evolutionary hypotheses at the species level. No such phylogeny has, however, been generated for any major plant group yet, but here we generate such a phylogeny for the palm family (Arecaceae). We do this using a novel Bayesian approach, estimating the validity of intra-generic taxonomic groupings as topological constraints to assist in placing species without genetic or morphological data. From these we implement those that are supported by genetic or morphological data for a given genus or for related genera. The intergeneric relationships in our new phylogeny are surprisingly different from earlier phylogenies in the placement of genera within tribes, but largely identical to previous findings in the deeper branches in the phylogeny, pointing to the need for incorporating phylogenetic uncertainty in analyses based on this phylogeny. Initial analyses of the new phylogeny suggest non-constancy in diversification rates over time within genera, with an apparent increase in diversification rate over time, but no evidence for any geographic variation in the magnitude of this increase. We hope that our study will stimulate further evolutionary or ecological studies using palms as study organisms as well as discussions of the optimal way to place the many species without genetic or morphological data. [ABSTRACT FROM AUTHOR]

The complex evolutionary history of the subtribe Physalinae is reflected in the poor resolution of the relationships of Physalis and the physaloid genera. We hypothesize that this low resolution is caused by recent evolutionary history in a complex geographic setting. The aims of this study were twofold: (1) To determine the phylogenetic relationships of the current genera recognized in Physalinae in order to identify monophyletic groups and resolve the physaloid grade; and (2) to determine the probable causes of the recent divergence in Physalinae. We conducted phylogenetic analyses with maximum likelihood (ML) and Bayesian inference with 50 Physalinae species and 19 others as outgroups, using morphological and molecular data from five plastid and two nuclear regions. A relaxed molecular clock was obtained from the ML topology and ancestral area reconstruction was conducted using the DEC model. The genera Chamaesaracha , Leucophysalis , and Physalis subgenus Rydbergis were recovered as monophyletic. Three clades, Alkekengi – Calliphysalis , Schraderanthus – Tzeltalia , and Witheringia – Brachistus , also received good support. However, even with morphological data and that of the DNA of seven regions, the tree was not completely resolved and many clades remained unsupported. Physalinae diverged at the end of the Miocene (∼9.22 Mya) with one trend indicating that the greatest diversification within the subtribe occurred during the last 5 My. The Neotropical region presented the highest probability (45%) of being the ancestral area of Physalinae followed by the Mexican Transition Zone (35%). During the Pliocene and Pleistocene, the geographical areas where species were found experienced significant geological and climatic changes, giving rise to rapid and relatively recent diversification events in Physalinae. Thus, recent origin, high diversification, and morphological complexity have contributed, at least with the currently available methods, to the inability to completely disentangle the phylogenetic relationships of Physalinae. [ABSTRACT FROM AUTHOR]

Most of the cultivated chenopods are polyploids, but their origin and evolutionary history are still poorly understood. Phylogenetic analyses of DNA sequences of four plastid regions, nrITS and nuclear 5S rDNA spacer region (NTS) of two tetraploid chenopods (2 n = 4 x = 36), Andean C. quinoa and North American C. berlandieri , and their diploid relatives allowed inferences of their origin. The phylogenetic analyses confirmed allotetraploid origin of both tetraploids involving diploids of two different genomic groups (genomes A and B) and suggested that these two might share very similar parentage. The hypotheses on the origin of the two allopolyploid species were further tested using genomic in situ hybridization (GISH). Several diploid Chenopodium species belonging to the two lineages, genome A and B, suggested by phylogenetic analyses, were tested as putative parental taxa. GISH differentiated two sets of parental chromosomes in both tetraploids and further corroborated their allotetraploid origin. Putative diploid parental taxa have been suggested by GISH for C. quinoa and C. berlandieri . Genome sizes of the analyzed allotetraploids fit nearly perfectly the expected additive values of the putative parental taxa. Directional and uniparental loss of rDNA loci of the maternal A-subgenome was revealed for both C. berlandieri and C. quinoa . [ABSTRACT FROM AUTHOR]

Observed Variability (OV) and Tree Independent Generation of Evolutionary Rates (TIGER) are quick and easy-to-apply tree-independent methods that have been proposed to provide unbiased estimates of each character’s rate of evolution and serve as the basis for excluding rapidly evolving characters. Both methods have been applied to multiple phylogenomic datasets, and in many cases the authors considered their trees inferred from the OV- and TIGER-delimited sub-matrices to be better estimates of the phylogeny than their trees based on all characters. In this study we use four sets of simulations and an empirical phylogenomic example to demonstrate that both methods share a systematic bias against characters with more symmetric distributions of character states, against characters with greater observed character-state space, and against large clades in the context of character conflict. As a result these methods can favor convergences and reversals over synapomorphy, exacerbate long-branch attraction, and produce mutually exclusive phylogenetic inferences that are dependent upon differential taxon sampling. We assert that neither OV nor TIGER should be relied upon to increase the ratio of phylogenetic to non-phylogenetic signal in a data matrix. We also assert that skepticism is warranted for empirical phylogenetic results that are based on OV- and/or TIGER-based character deletion wherein a small clade is supported after deletion of characters, yet is contradicted by a larger clade when the entire data matrix was analyzed. [ABSTRACT FROM AUTHOR]

In this study, molecular markers were used for the first time to study the genetic diversity of Turkish onion (Allium cepa L.) accessions. We used 83 turkish landraces, 3 breeding lines and 10 commercial varieties, in total 96 accessions, to study the genetic diversity. Bulked samples of 10 seeds were used to generate a representative profile of the accessions. Variability was evaluated at 46 microsatellite loci. We identified 308 alleles with these markers, out of which 303 were polymorphic. A dendrogram based on the UPGMA analysis grouped the 96 accessions into five main clusters. Dice's similarity coefficient ranged from 0.407 to 0.767 with an average of 0.587. The results showed that 44 out of the 46 SSR markers were convenient and polymorphic enough to distinguish all the studied accessions. [ABSTRACT FROM AUTHOR]

A phylogenetic analysis of the early branching lineages of the monocotyledons is performed using data from two plastid genes ( rbcL and matK), five mitochondrial genes ( atp1, ccmB, cob, mttB and nad5) and morphology. The complete matrix includes 93 terminals representing Acorus, the 14 families currently recognized within Alismatales, and numerous lineages of monocotyledons and other angiosperms. Total evidence analysis results in an almost completely resolved strict consensus tree, but all data partitions, genomic as well as morphological, are incongruent. The effects of RNA editing and potentially processed paralogous sequences are explored and discussed. Despite a decrease in incongruence length differences after exclusion of edited sites, the major data partitions remain significantly incongruent. The 14 families of Alismatales are all found to be monophyletic, but Acorus is found to be included in Alismatales rather than being the sister group to all other monocotyledons. The placement is strongly supported by the mitochondrial data, atp1 in particular, but it cannot be explained as an artifact caused by patterns of editing or by sampling of processed paralogues. [ABSTRACT FROM AUTHOR]

The first comprehensive phylogenetic study of the orchid genus Herminium and its allies is presented, based on seven molecular markers (nuclear internal transcribed spacer, Xdh, chloroplast matK, psaB, psbA-trnH, rbcL and trnL- F) and 37 morphological characters. Phylogenetic analyses indicate that Herminium as currently delimited is paraphyletic and that several genera are deeply nested within it. Based on parsimony analysis of total evidence, the generic circumscription of Herminium is expanded to include Androcorys, Bhutanthera, Frigidorchis and Porolabium. Apomorphic and plesiomorphic character states are identified for various clades recovered in this study. A few species currently wrongly assigned to Peristylus and Platanthera are here included in Herminium. All necessary new combinations are made. [ABSTRACT FROM AUTHOR]

Past phylogenetic studies of the monocot order Alismatales left several higher-order relationships unresolved. We addressed these uncertainties using a nearly complete genus-level sampling of whole plastid genomes (gene sets representing 83 protein-coding and ribosomal genes) from members of the core alismatid families, Tofieldiaceae and additional taxa (Araceae and other angiosperms). Parsimony and likelihood analyses inferred generally highly congruent phylogenetic relationships within the order, and several alternative likelihood partitioning schemes had little impact on patterns of clade support. All families with multiple genera were resolved as monophyletic, and we inferred strong bootstrap support for most inter- and intrafamilial relationships. The precise placement of Tofieldiaceae in the order was not well supported. Although most analyses inferred Tofieldiaceae to be the sister-group of the rest of the order, one likelihood analysis indicated a contrasting Araceae-sister arrangement. Acorus (Acorales) was not supported as a member of the order. We also investigated the molecular evolution of plastid NADH dehydrogenase, a large enzymatic complex that may play a role in photooxidative stress responses. Ancestral-state reconstructions support four convergent losses of a functional NADH dehydrogenase complex in Alismatales, including a single loss in Tofieldiaceae. [ABSTRACT FROM AUTHOR]

Candelariella placodizans is newly reported from China. It was collected on exposed rocks with mosses on the alpine areas of Taiwan and Yunnan Province, China at elevation between 3200-4400 m. Molecular phylogenetic analyses based on ITS rDNA sequences were also performed to confirm the monophyly of the Chinese populations with respect to already existing sequences of the species, and then further to examine their relationships to other members of the genus. An identification key to all 14 known taxa of Candelariella in China is provided. [ABSTRACT FROM AUTHOR]

Aldina (Leguminosae) is among the very few ecologically successful ectomycorrhizal lineages in a family largely marked by the evolution of nodulating symbiosis. The genus comprises 20 species predominantly distributed in Amazonia and has been traditionally classified in the tribe Swartzieae because of its radial flowers with an entire calyx and numerous free stamens. The taxonomy of Aldina is complicated due to its poor representation in herbaria and the lack of a robust phylogenetic hypothesis of relationship. Recent phylogenetic analyses of matK and trnL sequences confirmed the placement of Aldina in the 50-kb inversion clade, although the genus remained phylogenetically isolated or unresolved in the context of the evolutionary history of the main early-branching papilionoid lineages. We performed maximum likelihood and Bayesian analyses of combined chloroplast datasets ( matK , rbcL , and trnL ) and explored the effect of incomplete taxa or missing data in order to shed light on the enigmatic phylogenetic position of Aldina . Unexpectedly, a sister relationship of Aldina with the Andira clade ( Andira and Hymenolobium ) is revealed. We suggest that a new tribal phylogenetic classification of the papilionoid legumes should place Aldina along with Andira and Hymenolobium . These results highlight yet another example of the independent evolution of radial floral symmetry within the early-branching Papilionoideae, a large collection of florally heterogeneous lineages dominated by papilionate or bilaterally symmetric flower morphology. [ABSTRACT FROM AUTHOR]

The monospecific fern genus Nephopteris is restricted to four páramos in Colombia. Until now, its phylogenetic relationships have not been clarified, although morphological traits suggest that it belongs to the taenitidoid clade of the subfamily Pteridoideae in the Pteridaceae. We isolated four chloroplast ( atpA, chlL, rbcL, and rps4) loci of N. maxonii and performed maximum parsimony and maximum likelihood phylogenetic analyses, including a preliminary analysis based on rbcL of 424 accessions of leptosporangiate ferns. Then, we carried out separate and combined reconstructions for all four loci, focusing the sampling in the subfamily Pteridoideae (Pteridaceae). Our results show that Nephopteris belongs to the taenitidoid clade of the subfamily Pteridoideae and is nested in Jamesonia. Thus, the new combination Jamesonia maxonii is provided. Its dimorphic sterile and fertile leaves appear to be unique within the taenitidoids. Given that this species shares the same microhabitat with other Jamesonia species, it is unlikely that leaf shape evolution within the entire clade is a result of adaptive processes to páramo conditions. [ABSTRACT FROM AUTHOR]

Complicated history of gene duplication and loss brings challenge to molecular phylogenetic inference, especially in deep phylogenies. However, phylogenomic approaches, such as gene tree parsimony (GTP), show advantage over some other approaches in its ability to use gene families with duplications. GTP searches the ‘optimal’ species tree by minimizing the total cost of biological events such as duplications, but accuracy of GTP and phylogenetic signal in the context of different gene families with distinct histories of duplication and loss are unclear. To evaluate how different evolutionary properties of different gene families can impact on species tree inference, 3900 gene families from seven angiosperms encompassing a wide range of gene content, lineage-specific expansions and contractions were analyzed. It was found that the gene content and total duplication number in a gene family strongly influence species tree inference accuracy, with the highest accuracy achieved at either very low or very high gene content (or duplication number) and lowest accuracy centered in intermediate gene content (or duplication number), as the relationship can fit a binomial regression. Besides, for gene families of similar level of average gene content, those with relatively higher lineage-specific expansion or duplication rates tend to show lower accuracy. Additional correlation tests support that high accuracy for those gene families with large gene content may rely on abundant ancestral copies to provide many subtrees to resolve conflicts, whereas high accuracy for single or low copy gene families are just subject to sequence substitution per se. Very low accuracy reached by gene families of intermediate gene content or duplication number can be due to insufficient subtrees to resolve the conflicts from loss of alternative copies. As these evolutionary properties can significantly influence species tree accuracy, I discussed the potential weighting of the duplication cost by evolutionary properties of gene families in future GTP analyses. [ABSTRACT FROM AUTHOR]

The disjunction of floras between East Asia, Southeast North America, West North America, and Southwest Eurasia has been interpreted in terms of the fragmentation of a once continuous mixed mesophytic forest that occurred throughout the Northern Hemisphere due to the climatic and geological changes during the late Tertiary. The sword moss, Bryoxiphium , exhibits a distribution that strikingly resembles that of the mesophytic forest elements such as Liriodendron and is considered as the only living member of an early Tertiary flora in Iceland. These hypotheses are tested here using molecular dating analyses and ancestral area estimations. The results suggest that the extant range of Bryoxiphium results from the fragmentation of a formerly wider range encompassing North America and Southeast Asia about 10 million years ago. The split of continental ancestral populations is too recent to match with a continental drift scenario but is spatially and temporally remarkably congruent with that observed in Tertiary angiosperm relict species. The timing of the colonization of Iceland from Macaronesian ancestors, about two million years ago, is, however, incompatible with the hypothesis that Bryoxiphium is the only living member of an early Tertiary flora of the island. Alaska was recurrently colonized from East Asia. The ability of Bryoxiphium to overcome large oceanic barriers is further evidenced by its occurrence on remote oceanic archipelagos. In particular, Madeira was colonized twice independently from American and East Asian ancestors, respectively. The striking range disjunction of Bryoxiphium is interpreted in terms of its mating system, as the taxon exhibits a very singular pattern of spatial segregation of the sexes. [ABSTRACT FROM AUTHOR]

In this paper we investigate the biogeography of the temperate woody bamboos (Arundinarieae) using a densely-sampled phylogenetic tree of Bambusoideae based on six plastid DNA loci, which corroborates the previously discovered 12 lineages (I–XII) and places Kuruna as sister to the Chimonocalamus clade. Biogeographic analyses revealed that the Arundinarieae diversified from an estimated 12 to 14 Mya, and this was followed by rapid radiation within the lineages, particularly lineages IV, V and VI, starting from c. 7–8 Mya. It is suggested that the late Miocene intensification of East Asian monsoon may have contributed to this burst of diversification. The possibilities of the extant Sri Lankan and African temperate bamboo lineages representing ‘basal elements’ could be excluded, indicating that there is no evidence to support the Indian or African route for migration of temperate bamboo ancestors to Asia. Radiations from eastern Asia to Africa, Sri Lanka, and to North America all are likely to have occurred during the Pliocene, to form the disjunct distribution of Arundinarieae we observe today. The two African lineages are inferred as being derived independently from Asian ancestors, either by overland migrations or long-distance dispersals. Beringian migration may explain the eastern Asian–eastern North American disjunction. [ABSTRACT FROM AUTHOR]

Phylogenetic studies in Melastomataceae have demonstrated the need for taxonomic rearrangements in the current classification. Nonetheless, melastomes are among the most diverse groups of plants and several cases of known artificial taxa have been observed and awaiting further resolution. The Leandra s.str. clade, with ca. 200 species, includes the majority of the taxa traditionally treated in the genus Leandra and is almost restricted to eastern Brazil. In earlier studies, some attempts have been made to infer the relationships within Leandra s.str., but the sampling was sparse and the resolution low inside the clade. Here, we attempt to provide an improved phylogenetic hypothesis for this group on which to base further studies. Specifically, we provide a comprehensive taxon sampling and attempt to infer a species tree for this group, dissecting potential noise in the phylogenetic reconstruction, such as paralogy, rogue taxa, hybridization and incomplete lineage sorting. Our data set includes 126 ingroup species (192 terminals) and four partitions (six markers). We implement the ∗ BEAST model for species tree inference and perform several simulation methods to assess model fit and to discuss potential causes for the observed patterns. Major lineages of Leandra s.str. were delineated, a strictly bifurcating species tree model seems to not account for the observed data, and hybridization is very likely an important evolutionary force in this group. [ABSTRACT FROM AUTHOR]

The grade of early-diverging eudicots includes five major lineages: Ranunculales, Trochodendrales, Buxales, Proteales and Sabiaceae. To examine the evolution of plastome structure in early-diverging eudicots, we determined the complete plastome sequences of eight previously unsequenced early-diverging eudicot taxa, Pachysandra terminalis (Buxaceae), Meliosma aff. cuneifolia (Sabiaceae), Sabia yunnanensis (Sabiaceae), Epimedium sagittatum (Berberidaceae), Euptelea pleiosperma (Eupteleaceae), Akebia trifoliata (Lardizabalaceae), Stephania japonica (Menispermaceae) and Papaver somniferum (Papaveraceae), and compared them to previously published plastomes of the early-diverging eudicots Buxus , Tetracentron , Trochodendron , Nelumbo , Platanus , Nandina , Megaleranthis , Ranunculus , Mahonia and Macadamia . All of the newly sequenced plastomes share the same 79 protein-coding genes, 4 rRNA genes, and 30 tRNA genes, except for that of Epimedium , in which infA is pseudogenized and clpP is highly divergent and possibly a pseudogene. The boundaries of the plastid Inverted Repeat (IR) were found to vary significantly across early-diverging eudicots; IRs ranged from 24.3 to 36.4 kb in length and contained from 18 to 33 genes. Based on gene content, the IR was classified into six types, with shifts among types characterized by high levels of homoplasy. Reconstruction of ancestral IR gene content suggested that 18 genes were likely present in the IR region of the ancestor of eudicots. Maximum likelihood phylogenetic analysis of a 79-gene, 97-taxon data set that included all available early-diverging eudicots and representative sampling of remaining angiosperm diversity largely agreed with previous estimates of early-diverging eudicot relationships, but resolved Trochodendrales rather than Buxales as sister to Gunneridae , albeit with relatively weak bootstrap support, conflicting with what has been found for these three clades in most previous analyses. In addition, Proteales was resolved as sister to Sabiaceae with the highest support (bootstrap >90%) yet observed in plastome-scale phylogenetic analyses. [ABSTRACT FROM AUTHOR]

Tropical and subtropical amphi-Pacific disjunction is among the most fascinating distribution patterns, but received little attention. Here we use the fossil-rich Cinnamomum group, a primarily tropical and subtropical Asian lineage with some species distributed in Neotropics, Australasia and Africa to shed light upon this disjunction pattern. Phylogenetic and biogeographic analyses were carried out using sequences of three nuclear loci from 94 Cinnamomum group and 13 outgroup samples. Results show that although there are three clades within a monophyletic Cinnamomum group, Cinnamomum and previously recognized subdivisions within this genus were all rejected as natural groups. The Cinnamomum group appears to have originated in the widespread boreotropical paleoflora of Laurasia during the early Eocene (ca. 55 Ma). The formation and breakup of the boreotropics seems to have then played a key role in the formation of intercontinental disjunctions within the Cinnamomum group. The first cooling interval (50–48 Ma) in the late early Eocene resulted in a floristic discontinuity between Eurasia and North America causing the tropical and subtropical amphi-Pacific disjunction. The second cooling interval in the mid-Eocene (42–38 Ma) resulted in the fragmentation of the boreotropics within Eurasia, leading to an African–Asian disjunction. Multiple dispersal events from North into South America occurred from the early Eocene to late Miocene and a single migration event from Asia into Australia appears to have occurred in the early Miocene. [ABSTRACT FROM AUTHOR]

Karyotype evolution can be reconstructed by the characterization of chromosome morphology, based on the position of centromeres. Different karyotypes often reflect speciation events within phylogenies as they can establish crossing barriers between species. Hence, evolution of karyotypes often is congruent with splits and differentiation of clades within phylogenies of angiosperm genera. Here we study karyotype evolution in the big cosmopolitan genus Ranunculus and in related genera to test the hypothesis that karyotypes are congruent with major clades. We investigated karyotypes on mitoses of 36 species, evaluated literature records for additional 87 species, and reconstructed ancestral states by mapping karyotypes onto a published molecular phylogenetic tree. Altogether ten karyotypes can be discriminated as character states, eight based on the base number x = 8, and two on the base number x = 7. The ancestral type within Ranunculus is characterized by four metacentric and four submetacentric/subtelocentric chromosomes, and dominates in five major basal clades of Ranunculus ( R . subg. Auricomus ) and in four of the related genera ( Coptidium , Halerpestes , Kumlienia , and Trautvetteria ). Another four karyotypes are ancestral and predominant in two major clades within Ranunculus ( R . subg. Ranunculus ), while three further ones occur only on terminal branches of the buttercup phylogeny. Among related genera, Ficaria and Ceratocephala also show derived karyotypes. Karyotype morphology thus supports generic and infrageneric classifications based on molecular and morphological data. Karyotype evolution drives in general to increasing number of chromosomes with asymmetric arms, and to a reduction from x = 8 to x = 7 chromosomes. A review of interspecific homoploid hybridization in sympatric species, and of crossing experiments suggests enhanced crossability of species with the same karyotype and strong crossing barriers between those with different karyotypes. We conclude that karyotype evolution is a major driver of speciation and differentiation of clades within Ranunculus . [ABSTRACT FROM AUTHOR]

Cimicifuga nanchuanensis P. K. Hsiao (Ranunculaceae) has been regarded as an imperfectly known species. Based on critical examination of herbarium specimens and living plants we have determined that it is a morphologically distinctive species and that its geographical range is much wider than believed before, far from locally endemic to its type locality. Our cytological examination reveals the species to be a diploid (2n = 16). Our molecular phylogenetic analyses using nrDNA and cpDNA datasets confirm our morphological observations. As the generic concept and delimitation of Actaea L., in which Cimicifuga Wernisch. and Souliea Franch. are included, have also been strongly corroborated by our molecular phylogenetic analyses, here we adopt a broad Actaea and make a new combination for the species in question, i.e. Actaea nanchuanensis (P. K. Hsiao) J. P. Luo, Q. Yuan & Q. E. Yang. [ABSTRACT FROM AUTHOR]