scholarly journals Nuclear and Plastid DNA Sequence-based Molecular Phylogeography of Salvadora oleoides (Salvadoraceae) in Punjab, India

2016 ◽  
Author(s):  
Felix Bast ◽  
Navreet Kaur
Keyword(s):  
Tree Species ◽  
Sequence Data ◽  
Indian Subcontinent ◽  
Phylogenetic Analyses ◽  
Gene Tree ◽  
Plastid Dna ◽  
North India ◽  
Internal Transcribed Spacer Region ◽  
Relative Placement ◽  
The Arid Regions

AbstractSalvadora oleiodes is a tropical tree species belonging to the little-known family Salvadoraceae and distributed in the arid regions of Africa and Asia. Aims of our study were to trace the microevolutionary legacy of this tree species with the help of sequence-based multi-local phylogeography and to find the comparative placement of family Salvadoraceae within angiosperm clade malvids. A total 20 geographical isolates were collected from different regions of North India, covering a major part of its species range within the Indian Subcontinent. Sequence data from nuclear-encoded Internal Transcribed Spacer region (ITS1-5.8S-ITS2) and plastid-encoded trnL-F spacer region, were generated for this species for the first time in the world. ITS-based Bayesian phylogeographic analysis revealed the existence of four clades while trnL-F spacer based Bayesian analysis revealed one clade for this species distributed in the Indian subcontinent. Between these two loci, ITS revealed more distinct phylogeographic clades, indicating the phylogeographic utility of this locus for the systematics of Salvadoraceae. Phylogenetic analyzes based on trnL-F spacer suggested a synonymy of this species with Salvadora angustifolia. Maximum Likelihood gene tree based on ITS sequence data revealed that Salvadoraceae belongs to Sapindales rather than Brassicales. However, in the gene tree based on trnL-F spacer sequence, this family clustered within Brassicales. An evolutionary congruence of S. oleoides isolates across its range in North India is revealed in this study. Given the conflicting results on the relative placement of Salvadoraceae in Brassicales and Sapindales, the need for further phylogenetic analyses of malvids using supermatrix approach is highlighted.

scholarly journals Evolution of pollination syndromes and corolla symmetry in Balsaminaceae reconstructed using phylogenetic comparative analyses

2020 ◽  
Author(s):  
Saroj Ruchisansakun ◽  
Arne Mertens ◽  
Steven B Janssens ◽  
Erik F Smets ◽  
Timotheüs van der Niet
Keyword(s):  
Phylogenetic Trees ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Pollination Syndrome ◽  
Pollination Syndromes ◽  
Bee Pollination ◽  
Floral Symmetry ◽  
Considerable Uncertainty ◽  
Pollination Systems

Abstract Background and Aims Floral diversity as a result of plant–pollinator interactions can evolve by two distinct processes: shifts between pollination systems or divergent use of the same pollinator. Although both are pollinator driven, the mode, relative importance and interdependence of these different processes are rarely studied simultaneously. Here we apply a phylogenetic approach using the Balsaminaceae (including the species-rich genus Impatiens) to simultaneously quantify shifts in pollination syndromes (as inferred from the shape and colour of the perianth), as well as divergent use of the same pollinator (inferred from corolla symmetry). Methods For 282 species we coded pollination syndromes based on associations between floral traits and known pollination systems, and assessed corolla symmetry. The evolution of these traits was reconstructed using parsimony- and model-based approaches, using phylogenetic trees derived from phylogenetic analyses of nuclear ribosomal and plastid DNA sequence data. Key Results A total of 71 % of studied species have a bee pollination syndrome, 22 % a bimodal syndrome (Lepidoptera and bees), 3 % a bird pollination syndrome and 5 % a syndrome of autogamy, while 19 % of species have an asymmetrical corolla. Although floral symmetry and pollination syndromes are both evolutionarily labile, the latter shifts more frequently. Shifts in floral symmetry occurred mainly in the direction towards asymmetry, but there was considerable uncertainty in the pattern of shift direction for pollination syndrome. Shifts towards asymmetrical flowers were associated with a bee pollination syndrome. Conclusion Floral evolution in Impatiens has occurred through both pollination syndrome shifts and divergent use of the same pollinator. Although the former appears more frequent, the latter is likely to be underestimated. Shifts in floral symmetry and pollination syndromes depend on each other but also partly on the region in which these shifts take place, suggesting that the occurrence of pollinator-driven evolution may be determined by the availability of pollinator species at large geographical scales.

Senecio imbaburensis, proposed name for Lasiocephalus sodiroi in the genus Senecio (Asteraceae)

Phytotaxa ◽  
2013 ◽  
Vol 152 (1) ◽  
pp. 59
Author(s):  
Karol Marhold ◽  
Petr Sklenář
Keyword(s):  
Dna Sequence ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Dna Sequence Data ◽  
Number Of Species ◽  
The Andes

Lasiocephalus Willd. ex Schlechtendal (1818: 308), as traditionally circumscribed (e.g., by Cuatrecasas 1978, Dušková et al. 2010), is a neotropical genus of ca 25 species confined to the Andes and distributed from Venezuela to Bolivia. Nevertheless, recent studies by Pelser et al. (2007, 2010) have shown that based on phylogenetic analyses of nrITS and plastid DNA sequence data, species of the genus Lasiocephalus are deeply embedded in Senecio Linnaeus (1753: 866), and, consequently, should be transferred into this latter genus. In fact, a number of species of Lasiocephalus were originally described as Senecio or had been, at some point, transferred into Senecio so only few transfers are necessary.

Hybridization in the Temperate Bamboos (Poaceae: Bambusoideae: Arundinarieae): A Phylogenetic Study Using AFLPs and cpDNA Sequence Data

2021 ◽  
Vol 46 (1) ◽  
pp. 48-69
Author(s):  
Jimmy K. Triplett ◽  
Lynn G. Clark
Keyword(s):  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Intergeneric Hybrid ◽  
Plastid Dna ◽  
Sensu Stricto ◽  
Phylogenetic Study ◽  
Aflp Data ◽  
The North ◽  
Cpdna Sequence

Abstract—The temperate bamboos are a taxonomically difficult group with nearly 600 species in approximately 30 genera and at least 12 constituent lineages. In this study, phylogenetic relationships were explored using amplified fragment length polymorphism (AFLP) data in comparison with a phylogeny based on plastid DNA sequences, with an emphasis onArundinariaof North America and its allies in East Asia (theArundinariaclade). Molecular analyses involved 248 individuals in 10 genera and 60 species. Hybridization was detected both within and among genera. Comparative analyses indicated hybrid origins for species in several widespread and well-known genera, includingHibanobambusa,Sasaella, andSemiarundinaria. Evidence also indicated thatPseudosasa japonica(the type species ofPseudosasa) is an intergeneric hybrid involvingPleioblastusandSasamorpha. In addition, cryptic hybrids were detected within and amongPleioblastus,Sasa, andSasamorpha. After accounting for hybrids, phylogenetic analyses of AFLP data provided resolution for core lineages in theArundinariaclade, includingPleioblastussensu stricto,Sasas. s., andSasamorpha.AFLP data also provided evidence for the monophyly of the North American cane bamboos (Arundinaria, three species) but failed to identify their closest relative among the East Asian taxa. The broader evolutionary implications of hybridization in the temperate bamboos are discussed along with recommendations for future studies.

scholarly journals Cryptic species of Curvularia in the culture collection of the Queensland Plant Pathology Herbarium

MycoKeys ◽  
2018 ◽  
Vol 35 ◽  
pp. 1-25 ◽  
Author(s):  
Yu Pei Tan ◽  
Pedro W. Crous ◽  
Roger G. Shivas
Keyword(s):  
Plant Pathology ◽  
Dna Sequences ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Culture Collection ◽  
Internal Transcribed Spacer Region ◽  
Translation Elongation ◽  
Air Sample ◽  
Elongation Factor 1

Several unidentified specimens of Curvularia deposited in the Queensland Plant Pathology Herbarium were re-examined. Phylogenetic analyses based on sequence data of the internal transcribed spacer region, partial fragments of the glyceraldehyde-3-phosphate dehydrogenase and the translation elongation factor 1-α genes, supported the introduction of 13 novel Curvularia species. Eight of the species described, namely, C.beasleyi sp. nov., C.beerburrumensis sp. nov., C.eragrosticola sp. nov., C.kenpeggii sp. nov., C.mebaldsii sp. nov., C.petersonii sp. nov., C.platzii sp. nov. and C.warraberensis sp. nov., were isolated from grasses (Poaceae) exotic to Australia. Only two species, C.lamingtonensis sp. nov. and C.sporobolicola sp. nov., were described from native Australian grasses. Two species were described from hosts in other families, namely, C.coatesiae sp. nov. from Litchichinensis (Sapindaceae) and C.colbranii sp. nov. from Crinumzeylanicum (Amaryllidaceae). Curvulariareesii sp. nov. was described from an isolate obtained from an air sample. Furthermore, DNA sequences from ex-type cultures supported the generic placement of C.neoindica and the transfer of Drechsleraboeremae to Curvularia.

Kamalia indica, a new genus and species belonging to Diaporthales (Ascomycota, Fungi) described based on morphology and molecular phylogeny

Phytotaxa ◽  
2019 ◽  
Vol 425 (4) ◽  
pp. 233-243
Author(s):  
SHIWALI RANA ◽  
SANJAY KUMAR SINGH
Keyword(s):  
Dna Sequences ◽  
Internal Transcribed Spacer ◽  
New Genus ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Large Subunit ◽  
Type Specimen ◽  
Morphological Description ◽  
Fungal Culture ◽  
Internal Transcribed Spacer Region

A fungal taxa isolated from leaf spots of Mallotus philippensis from Kangra district of North-Western Himalayan region of India is established as a new genus based on morphological characters of asexual-morphs, cultural characteristics and phylogenetic analyses of the partial nuclear ribosomal 28S large subunit (LSU) and internal transcribed spacer (ITS) rDNA sequence data. The generic placement of the genus has been determined based on DNA sequences from authenticated isolates. The present taxon has turned out to be distinct, showing nearly 90% identity with other known genera in Diaporthales based on nrDNA internal transcribed spacer region. The morphological description is provided for the new taxa and compared with the similar taxa belonging to the order Diaporthales. The culture was found to show heavy sporulation in all kind of media. The type specimen and ex type culture have been deposited in the Ajrekar Mycological Herbarium (AMH) and National Fungal Culture Collection of India (NFCCI-WDCM 932), respectively.

scholarly journals Botryosphaeriaceae Species Associated With Cankers and Dieback Symptoms of Acacia mangium and Pinus caribaea var. hondurensis in Venezuela

Plant Disease ◽  
2016 ◽  
Vol 100 (12) ◽  
pp. 2455-2464 ◽  
Author(s):  
J. R. Úrbez-Torres ◽  
F. Castro-Medina ◽  
S. R. Mohali ◽  
W. D. Gubler
Keyword(s):  
Dna Sequences ◽  
Tree Species ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
Acacia Mangium ◽  
Forest Tree ◽  
Pinus Caribaea ◽  
Internal Transcribed Spacer Region ◽  
Forest Tree Species ◽  
Wide Range

Several species in the Botryosphaeriaceae family cause wood stain, cankers, and dieback of trunks and branches in a wide range of forest tree species. The aim of this study was to characterize the botryosphaeriaceous fungi associated with decline symptoms observed in Acacia mangium and Pinus caribaea var. hondurensis, two economically important forest tree species grown in commercial plantations in Venezuela. Fungi isolated from symptomatic samples collected from both hosts in commercial sites were identified based on their morphology and DNA sequences of the internal transcribed spacer region (ITS1-5.8S-ITS2) and part of the β-tubulin and translation elongation factor 1-α genes. Lasiodiplodia theobromae and L. venezuelensis were routinely isolated from A. mangium and P. caribaea var. hondurensis. Additionally, the novel species Diplodia guayanensis was isolated and characterized from symptomatic and asymptomatic tissues of A. mangium. Multigene phylogenetic analyses along with restriction fragment length polymorphism studies further supported the identification of these species. A pathogenicity study was conducted under natural conditions and 12 weeks after inoculation all Botryosphaeriaceae spp. were shown to be highly virulent on A. mangium. Contrary, no lesions were observed in the wood of P. caribaea var. hondurensis when inoculated with L. theobromae and L. venezuelensis. However, both species were consistently reisolated from the asymptomatic tissue beyond the inoculation point. This study contributes to a better understand the role that species in the Botryosphaeriaceae play on disease symptoms and dieback of A. mangium and P. caribaea var. hondurensis from plantations in eastern Venezuela.

scholarly journals Phylogenetic analysis of Australian species of Veronica (V. section Labiatoides; Plantaginaceae)

2012 ◽  
Vol 25 (5) ◽  
pp. 353 ◽  
Author(s):  
Dirk C. Albach ◽  
Barbara G. Briggs
Keyword(s):  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Woody Species ◽  
Plastid Dna ◽  
Hybrid Origin ◽  
Herbaceous Species ◽  
Dna Sequence Data ◽  
Australian Species ◽  
Moist Forest ◽  
Forest Habitats

Phylogenetic analyses of DNA-sequence data have revealed that the southern hemisphere species of Veronica are derived from within the northern hemisphere Veronica clade. Previous analyses focussed on the species in New Zealand and included at maximum 7 of 23 species of section Labiatoides from Australia. In the present study, we used nuclear ribosomal-ITS and plastid ndhF–rpl32-spacer sequence data of all species currently recognised in Australia to analyse phylogenetic patterns. Most importantly, herbaceous species from coastal calcareous sands or limestone habitats do not form a clade with those from shady, moist forest habitats, as formerly believed, but seem to be independently derived from woody species. Incongruence between results from nuclear- and plastid-DNA markers suggest hybridisation to be an important factor in the evolution of the group. Our sample of V. parnkalliana included alleles similar to V. decorosa and V. novae-hollandiae at both loci, which suggests a hybrid origin.

scholarly journals Two Novel Fungal Symbionts Fusarium kuroshium sp. nov. and Graphium kuroshium sp. nov. of Kuroshio Shot Hole Borer (Euwallacea sp. nr. fornicatus) Cause Fusarium Dieback on Woody Host Species in California

Plant Disease ◽  
2018 ◽  
Vol 102 (6) ◽  
pp. 1154-1164 ◽  
Author(s):  
Francis Na ◽  
Joseph D. Carrillo ◽  
Joey S. Mayorquin ◽  
Cedric Ndinga-Muniania ◽  
Jason E. Stajich ◽  
...  
Keyword(s):  
Rna Polymerase Ii ◽  
Tree Species ◽  
Tree Mortality ◽  
Phylogenetic Analyses ◽  
Elongation Factor ◽  
San Diego County ◽  
Internal Transcribed Spacer Region ◽  
Branch Dieback ◽  
Fusarium Dieback ◽  
Disease Complexes

Shot hole borer (SHB)-Fusarium dieback (FD) is a new pest-disease complex affecting numerous tree species in California and is vectored by two distinct, but related ambrosia beetles (Euwallacea sp. nr. fornicatus) called polyphagous shot hole borer (PSHB) and Kuroshio shot hole borer (KSHB). These pest-disease complexes cause branch dieback and tree mortality on numerous wildland and landscape tree species, as well as agricultural tree species, primarily avocado. The recent discovery of KSHB in California initiated an investigation of fungal symbionts associated with the KSHB vector. Ten isolates of Fusarium sp. and Graphium sp., respectively, were recovered from the mycangia of adult KSHB females captured in three different locations within San Diego County and compared with the known symbiotic fungi of PSHB. Multigene phylogenetic analyses of the internal transcribed spacer region (ITS), translation elongation factor-1 alpha (TEF1-α), and RNA polymerase II subunit (RPB1, RPB2) regions as well as morphological comparisons revealed that two novel fungal associates Fusarium kuroshium sp. nov. and Graphium kuroshium sp. nov. obtained from KSHB were related to, but distinct from the fungal symbionts F. euwallaceae and G. euwallaceae associated with PSHB in California. Pathogenicity tests on healthy, young avocado plants revealed F. kuroshium and G. kuroshium to be pathogenic. Lesion lengths from inoculation of F. kuroshium were found to be significantly shorter compared with those caused by F. euwallaceae, while no difference in symptom severity was detected between Graphium spp. associated with KSHB and PSHB. These findings highlight the pest disease complexes of KSHB-FD and PSHB-FD as distinct, but collective threats adversely impacting woody hosts throughout California.

Cymbidium brevifolium (Orchidaceae; Epidendroideae), a new species from China: evidence from morphological and molecular data

Phytotaxa ◽  
2020 ◽  
Vol 464 (3) ◽  
pp. 236-242
Author(s):  
ZHUANG ZHOU ◽  
DIYANG ZHANG ◽  
GUI-ZHEN CHEN ◽  
XIA YU ◽  
CHENG-RU LI ◽  
...  
Keyword(s):  
New Species ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Plastid Dna ◽  
Detailed Comparison ◽  
Molecular Data ◽  
The Status ◽  
Nuclear Its ◽  
Morphological And Molecular Data ◽  
A New Species

A new orchid species, Cymbidium brevifolium, from Hubei Province, China, is described and illustrated based on morphological and molecular analyses. A detailed comparison between the newly discovered orchid and other members of Cymbidium was conducted. The new orchid is distinct from all other recognized species in Cymbidium. Phylogenetic analyses based on nuclear (ITS) and plastid DNA (matK and rbcL) sequence data support the status of C. brevifolium as a new species, which is sister to C. faberi.

Divergence, diversity and species of the Australasian Callitris (Cupressaceae) and allied genera: evidence from ITS sequence data

2003 ◽  
Vol 16 (4) ◽  
pp. 505 ◽  
Author(s):  
M. G. Pye ◽  
P. A. Gadek ◽  
K. J. Edwards
Keyword(s):  
Strong Evidence ◽  
Internal Transcribed Spacer ◽  
New Caledonia ◽  
Sequence Data ◽  
Phylogenetic Analyses ◽  
Its Sequence ◽  
Internal Transcribed Spacer Region ◽  
Diverse Range ◽  
26S Rdna ◽  
Close Relationship

Callitris Vent. is the most speciose of the Southern Hemisphere genera of Cupressaceae, occupying a diverse range of habitats within Australia and New Caledonia and is closely allied to Actinostrobus Miq. and the monotypic New Caledonian genus Neocallitropsis Florin. Results of phylogenetic analyses of 18S–26S rDNA internal transcribed spacer region sequences for representatives of 12 of the 18 currently recognised species of Callitris, two of the three Actinostrobus species and the single known species of Neocallitropsis help to clarify major lineages and relationships in this group. ITS data provide strong evidence against the monophyly of Callitris as currently circumscribed, with the strongest evidence being for the inclusion of the New Caledonian monotypic species Neocallitropsis pancheri (Carriere) de Laubenfels. This species shares a close relationship with C. sulcata (Parl.) Schltr. Three representatives of Actinostrobus are monophyletic and are placed in a polytomy with C.�drummondii (Parl.) F.Muell., although indels provide some support for the early divergence of Actinostrobus in this group. Remaining sampled members of Callitris form a weakly supported clade, with C. macleayana (F.Muell.) F.Muell. sister to a highly robust core Callitris. Relationships within this core Callitris are unresolved; however, the following seven lineages are supported: C. rhomboidea R.Br. ex Rich.; C. muelleri (Parl.) F.Muell., C. oblonga Rich. and C. endlicheri (Parl.) F.M. Bailey; C. gracilis R.T. Baker, C. glaucophylla Thompson & Johnson and C.�tuberculata R.Br. ex R.T. Baker & Smith; C. intratropica Baker & Smith; and C. columellaris F.Muell. There has been a marked increase in the rate of divergence of ITS sequences during the evolution of those populations assigned to C. intratropica, which perhaps reflects speciation processes within this widely distributed group.

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