Phylogenetic analysis of chloroplast rps16 intron sequences reveals relationships within the woody southern African Apiaceae subfamily Apioideae

1999 ◽  
Vol 77 (8) ◽  
pp. 1120-1135 ◽  
Author(s):  
Stephen R Downie ◽  
Deborah S Katz-Downie
Keyword(s):  
Southern Africa ◽  
Sequence Divergence ◽  
Evolutionary Relationships ◽  
Molecular Evidence ◽  
Neighbor Joining ◽  
Molecular Systematic ◽  
Rps16 Intron ◽  
Place Of Origin ◽  
High Level ◽  
Rps16 Intron Sequences

Evolutionary relationships among 48 genera of Apiaceae (Umbelliferae) were inferred using maximum parsimony, maximum-likelihood, and neighbor-joining analyses of chloroplast DNA rps16 intron and adjacent rps16 3prime exon sequences. Emphasis was placed on woody members of Apiaceae subfamily Apioideae endemic to southern Africa, a region hypothesized to be the place of origin of this largely herbaceous subfamily. The resultant phylogenies were highly concordant and indicate that the apioid genera Polemanniopsis and Steganotaenia form a clade sister to Apiaceae subfamily Saniculoideae. The African genera Anginon, Dracosciadium, Glia, Heteromorpha, and Polemannia also comprise a clade and likely represent the most basal elements within Apioideae. Heteromorpha, however, is not monophyletic, with Heteromorpha arborescens (Spreng.) Cham. & Schltdl. var. abyssinica (A. Rich.) H. Wolff and Heteromorpha arborescens (Spreng.) Cham. & Schltdl. var. arborescens arising in separate subclades. Progressing up the trees, Annesorhiza then Bupleurum fall as successive sister taxa to all remaining Apioideae. The major clades recognized within subfamily Apioideae are largely congruent with those inferred using other types of molecular evidence. Sequence divergence is similar to that of other chloroplast introns, including being generally low among congeners and woody taxa. While the rps16 intron has seen very little use in molecular systematic studies to date, this study demonstrates its ability to discern high-level relationships within Apiaceae.Key words: Apiaceae, Apioideae, chloroplast rps16 intron, phylogeny, southern Africa, Umbelliferae.

scholarly journals Group AStreptococcusT Antigens Have a Highly Conserved Structure Concealed under a Heterogeneous Surface That Has Implications for Vaccine Design

2019 ◽  
Vol 87 (6) ◽  
Author(s):  
Paul G. Young ◽  
Jeremy M. Raynes ◽  
Jacelyn M. Loh ◽  
Thomas Proft ◽  
Edward N. Baker ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Sequence Divergence ◽  
Structural Similarity ◽  
T Antigen ◽  
T Antigens ◽  
Content Type ◽  
Group A ◽  
Efficacious Vaccine ◽  
High Level ◽  
Conserved Core

ABSTRACTGroup AStreptococcus(GAS) (Streptococcus pyogenes) is an important human pathogen associated with significant global morbidity and mortality for which there is no safe and efficacious vaccine. The T antigen, a protein that polymerizes to form the backbone of the GAS pilus structure, is a potential vaccine candidate. Previous surveys of theteegene, which encodes the T antigen, have identified 21 differentteetypes and subtypes such that any T antigen-based vaccine must be multivalent and carefully designed to provide broad strain coverage. In this study, the crystal structures of three two-domain T antigens (T3.2, T13, and T18.1) were determined and found to have remarkable structural similarity to the previously reported T1 antigen, despite moderate overall sequence similarity. This has enabled reliable modeling of all major two-domain T antigens to reveal that T antigen sequence variation is distributed along the full length of the protein and shields a highly conserved core. Immunoassays performed with sera from immunized animals and commercial T-typing sera identified a significant cross-reactive antibody response between T18.1, T18.2, T3.2, and T13. The existence of shared epitopes between T antigens, combined with the remarkably conserved structure and high level of surface sequence divergence, has important implications for the design of multivalent T antigen-based vaccines.

scholarly journals Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers

Forests ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 543
Author(s):  
Shijing Feng ◽  
Jinshuang Niu ◽  
Zhenshan Liu ◽  
Lu Tian ◽  
Xiangyuan Wang ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Genetic System ◽  
Haplotype Network ◽  
Evolutionary Relationships ◽  
Genetic Profile ◽  
Coding Region ◽  
Demographic Trends ◽  
Evolutionary Forces ◽  
High Level

Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.

Gelidium guimaraesiae sp. nov. (Gelidiaceae, Rhodophyta) from the Western Atlantic segregated from G. floridanum by morphological and molecular evidence

Phytotaxa ◽  
2019 ◽  
Vol 388 (4) ◽  
pp. 275 ◽  
Author(s):  
BEATRIZ BRUNELLI ◽  
DANIELA MILSTEIN ◽  
SUNG M. BOO ◽  
MUTUE T. FUJII
Keyword(s):  
Dna Sequences ◽  
Sequence Divergence ◽  
Molecular Data ◽  
Brazilian Coast ◽  
Molecular Evidence ◽  
Similar Species ◽  
Western Atlantic ◽  
Gelidium Floridanum ◽  
Morphological And Molecular Data ◽  
A New Species

The Gelidium species are susceptible to a great phenotypic plasticity. In this genus, studies integrating morphological and molecular data have been increasingly used to define species. To date nine Gelidium species are reported along the Brazilian coast. Gelidium floridanum is the most frequently recorded species in Brazilian but it is also often confused with morphologically similar species, especially in the field or when reproductive structures are absent. In this study we analyzed specimens from Brazil previously identified as G. floridanum based on the morphological and molecular data (cox1 and rbcL DNA sequences). Newly collected specimens from Brazil showed a DNA sequence divergence from G. floridanum in the order of 1.0–1.4% for rbcL and 4.2% for cox1, enough to be considered a new species, here described as Gelidium guimaraesiae sp. nov.

The rediscovery and conservation status of the Bahian giant tree rat Phyllomys unicolor (Mammalia: Rodentia: Echimyidae) in the Atlantic forest of Brazil

Zootaxa ◽  
2007 ◽  
Vol 1638 (1) ◽  
pp. 51-57 ◽  
Author(s):  
YURI L.R. LEITE ◽  
SIMONE LÓSS ◽  
RENAN P. REGO ◽  
LEONORA P. COSTA ◽  
CIBELE R. BONVICINO
Keyword(s):  
Atlantic Forest ◽  
Conservation Status ◽  
Sequence Divergence ◽  
Field Studies ◽  
Single Specimen ◽  
Species List ◽  
Eastern Brazil ◽  
Mitochondrial Cytochrome B ◽  
Nineteeth Century ◽  
High Level

The Bahian giant tree rat Phyllomys unicolor (Wagner) was described from a single specimen collected in the early nineteeth century, and it has not been recorded since. It was included on the Brazilian endangered species list, and considered extinct by some. Here we report the rediscovery of P. unicolor around the type locality in the Atlantic forest of southeastern Bahia, eastern Brazil. We trapped only one young individual during seven expeditions to ten localities in the area. The phylogenetic distinctiveness of this taxon based on the mitochondrial cytochrome b gene is clear, in spite of uncertainties regarding clade support. The evolutionary uniqueness of P. unicolor was confirmed by a high level of sequence divergence from congeneric species. We propose that the Bahian giant tree rat should be globally listed as Critically Endangered by the World Conservation Union. Phyllomys unicolor seems to be restricted to swamp forests and it does not occur in any protected area. Intensive field studies should be carried out in the region to locate populations and to study ecological attributes of this species. The rediscovery of P. unicolor draws attention to the biological importance and the lack of protected areas in this region of the Atlantic forest.

Characterisation of an Iberian population of Rhyssocolpus iuventutis Andrássy, 1971 (Dorylaimida: Nordiidae), with a revised taxonomy of the genus

Nematology ◽  
2015 ◽  
Vol 17 (2) ◽  
pp. 139-153 ◽  
Author(s):  
Reyes Peña-Santiago ◽  
Pablo Guerrero ◽  
Gracia Liébanas ◽  
María del Carmen García ◽  
Teresa Palomeque ◽  
...  
Keyword(s):  
Common Ancestor ◽  
Ssu Rdna ◽  
Morphological Data ◽  
Recent Common Ancestor ◽  
Integrative Approach ◽  
Evolutionary Relationships ◽  
Molecular Evidence ◽  
Rdna Sequences ◽  
Iberian Population ◽  
Emended Diagnosis

The identity and evolutionary relationships of the genus Rhyssocolpus are analysed and discussed using an integrative approach including morphological data and partial SSU-rDNA sequences. An Iberian population of R. iuventutis is characterised in detail, providing the first SEM observations of the genus. New sequences of the genera Enchodelus and Rhyssocolpus are provided for comparative purposes. Both morphological and molecular evidence support a separate status for the aforementioned two genera and Heterodorus, of which the latter and Rhyssocolpus shared a recent common ancestor, whereas Enchodelus did not, as had been traditionally assumed, occupy a close position. The Nordiidae is confirmed to be an artificial taxon. The taxonomy of Rhyssocolpus is revised and an emended diagnosis, updated list of species, key to their identification and compendium of their morphometrics are provided. Some nomenclatorial changes are also proposed: R. alleni and R. paradoxus are retained under Eudorylaimus, their original genus, whereas R. brasiliensis is transferred to Eudorylaimus as E. brasiliensis (Meyl, 1956) comb. n.

scholarly journals Cryptic species of Archinome (Annelida: Amphinomida) from vents and seeps

2013 ◽  
Vol 280 (1770) ◽  
pp. 20131876 ◽  
Author(s):  
Elizabeth Borda ◽  
Jerry D. Kudenov ◽  
Pierre Chevaldonné ◽  
James A. Blake ◽  
Daniel Desbruyères ◽  
...  
Keyword(s):  
Hydrothermal Vent ◽  
Species Delimitation ◽  
Hydrothermal Vents ◽  
Evolutionary Relationships ◽  
Molecular Evidence ◽  
Mitochondrial Cytochrome ◽  
East Pacific ◽  
The Pacific ◽  
First Time ◽  
Galapagos Rift

Since its description from the Galapagos Rift in the mid-1980s, Archinome rosacea has been recorded at hydrothermal vents in the Pacific, Atlantic and Indian Oceans. Only recently was a second species described from the Pacific Antarctic Ridge. We inferred the identities and evolutionary relationships of Archinome representatives sampled from across the hydrothermal vent range of the genus, which is now extended to cold methane seeps. Species delimitation using mitochondrial cytochrome c oxidase subunit I (COI) recovered up to six lineages, whereas concatenated datasets (COI, 16S, 28S and ITS1) supported only four or five of these as clades. Morphological approaches alone were inconclusive to verify the identities of species owing to the lack of discrete diagnostic characters. We recognize five Archinome species, with three that are new to science. The new species, designated based on molecular evidence alone, include: Archinome levinae n. sp., which occurs at both vents and seeps in the east Pacific, Archinome tethyana n. sp., which inhabits Atlantic vents and Archinome jasoni n. sp., also present in the Atlantic, and whose distribution extends to the Indian and southwest Pacific Oceans. Biogeographic connections between vents and seeps are highlighted, as are potential evolutionary links among populations from vent fields located in the east Pacific and Atlantic Oceans, and Atlantic and Indian Oceans; the latter presented for the first time.

scholarly journals Young adults in Poland – the coming of age of a generation of responsible food consumers?

2020 ◽  
Vol 2020 (146) ◽  
pp. 373-391
Author(s):  
Małgorzata PINK ◽  
◽  
Łukasz PALUCH ◽  
Katarzyna KOKOSZKA ◽  
◽  
...  
Keyword(s):  
Young Adults ◽  
Institutional Environment ◽  
Coming Of Age ◽  
Food Prices ◽  
Easy Access ◽  
Large Area ◽  
Plastic Bags ◽  
Production And Consumption ◽  
Place Of Origin ◽  
High Level

Purpose: The aim of the study was to diagnose attitudes and consumption behaviors among the young adults, regarding food consumption in Poland. Design/methodology/approach: 483 respondents took a part in the research. They were students of three Cracovian universities, representing all voivodships in Poland. The research instrument consisted of two types of questions: traditional closed survey questions and a series of projection questions, based on fictional characters, which the respondents had to assess and determine the degree of identification with the attitudes and behaviors described. Findings: The research revealed some akrasia. The relatively high level of awareness regarding the effects of unsustainable production and consumption of young adults did not translate into consumption behavior of a sustainable nature. The curiosity regarding origin of the product and its composition turned out to be low, as was the feeling of responsibility for their own decisions. There was a tendency to expect the transition of responsibility to food producers and the institutional environment. Young adults pay special attention to food prices and easy access to shopping. Local marketplaces are a niche shopping place. The majority of food is purchased in large-area stores, where consumers are not informed about the place of origin of food. The respondents group is characterized by high outside-diagonality, solutions forcing more sustainable behavior, for example, the payment for plastic bags, the need for recycling of waste meet with wide acceptance. Originality/value: The research revealed enforcing proecological behaviors by institutions seems to be a more effective than building consumer awareness.

scholarly journals ViralRecall: A Flexible Command-Line Tool for the Detection of Giant Virus Signatures in Omic Data

2020 ◽  
Author(s):  
Frank O Aylward ◽  
Mohammad Moniruzzaman
Keyword(s):  
Sequence Divergence ◽  
High Sensitivity ◽  
Giant Virus ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Bioinformatic Tool ◽  
Command Line Tool ◽  
High Level ◽  
Omic Data ◽  
Eukaryotic Genomes

Giant viruses are widespread in the biosphere and play important roles in biogeochemical cycling and host genome evolution. Also known as Nucleo-Cytoplasmic Large DNA Viruses (NCLDV), these eukaryotic viruses harbor the largest and most complex viral genomes known. Recent studies have shown that NCLDV are frequently abundant in metagenomic datasets, and that sequences derived from these viruses can also be found endogenized in diverse eukaryotic genomes. The accurate detection of sequences derived from NCLDV is therefore of great importance, but this task is challenging owing to both the high level of sequence divergence between NCLDV families and the extraordinarily high diversity of genes encoded in their genomes, including some encoding for metabolic or translation-related functions that are typically found only in cellular lineages. Here we present ViralRecall, a bioinformatic tool for the identification of NCLDV signatures in omic data. This tool leverages a library of Giant Virus Orthologous Groups (GVOGs) to identify sequences that bear signatures of NCLDV. We demonstrate that this tool can effectively identify NCLDV sequences with high sensitivity and specificity. Moreover, we show that it can be useful both for removing contaminating sequences in metagenome-assembled viral genomes as well as the identification of eukaryotic genomic loci that derived from NCLDV. ViralRecall is written in Python 3.5 and is freely available on GitHub: https://github.com/faylward/viralrecall.

Amana baohuaensis (Liliaceae), a new species from East China

Phytotaxa ◽  
2019 ◽  
Vol 427 (1) ◽  
pp. 43-50 ◽  
Author(s):  
LONG WANG ◽  
QIAN XING ◽  
GENG-YU LU ◽  
XU LU ◽  
QUN ZHAO ◽  
...  
Keyword(s):  
New Species ◽  
Phylogenetic Analyses ◽  
Jiangsu Province ◽  
East China ◽  
Similar Species ◽  
Rps16 Intron ◽  
Nuclear Its ◽  
A New Species ◽  
Rps16 Intron Sequences

Amana baohuaensis is described and illustrated as a new species from Jurong City, Jiangsu Province, East China. The new species is morphologically similar to A. edulis, but differs from the latter by having three verticillate linear bracts, white or purple-red solitary flowers, and purplish-brown anthers. Phylogenetic analyses based on nuclear ITS, chloroplast matK and rps16 intron sequences confirmed that this new species is distinct from morphologically similar species.

Morphological and molecular evidence for the recognition of Caloglossa fonticola sp. nov. (Delesseriaceae, Rhodophyta) from an underground spring in Guangxi, China

Phytotaxa ◽  
2021 ◽  
Vol 522 (1) ◽  
pp. 15-26
Author(s):  
KUN-PENG FANG ◽  
FANG-RU NAN ◽  
JIA FENG ◽  
QI LIU ◽  
XU-DONG LIU ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Dna Sequences ◽  
Sequence Divergence ◽  
Molecular Evidence ◽  
Unique Combination ◽  
High Sequence Divergence ◽  
Molecular Phylogenetic ◽  
Freshwater Habitats ◽  
Globally Distributed ◽  
Lateral Axis

Caloglossa (Ceramiales, Rhodophyta) is a globally distributed euryhaline red macroalgal genus. However, only a few Caloglossa species have been documented in permanent freshwater habitats. Here, a new Caloglossa species, Caloglossa fonticola sp. nov., is described and illustrated from an underground spring in Bama County, Guangxi, China, based on morphological observations and molecular phylogenetic analysis. The new species is morphologically distinguishable from other species in the genus by a unique combination of character states, including thallus internodal blades linear, hardly or slightly constricted at nodes, adventitious branches and endogenous branches both absent, and unicellular rhizoids forming from clusters of wing cells arising from the first three axial cells of the main axis and lateral axis. Phylogenetic analysis based on rbcL and LSU rRNA DNA sequences indicated that Caloglossa fonticola was nested in a well-supported clade with Caloglossa bengalensis (Bootstrap supports for ML/posterior probabilities for BI: rbcL-98/1.00, LSU-100/1.00), with high sequence divergence between these two species (8.2–8.4% for rbcL and 3.2% for LSU), supporting its specific status. This is the first species of the genus Caloglossa reported in spring water habitats. The description of C. fonticola expands the known diversity of Caloglossa.

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