Supermatrix analyses and molecular clock rooting of Fabales: Exploring the effects of outgroup choice and long branch attraction on topology

Botany ◽  
2020 ◽  
Vol 98 (4) ◽  
pp. 231-247
Author(s):  
Deniz Aygoren Uluer ◽  
Félix Forest ◽  
Julie A. Hawkins
Keyword(s):  
Molecular Clock ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Long Branch Attraction ◽  
Network Analyses ◽  
Branch Lengths ◽  
Group A ◽  
First Time

Fabales is a cosmopolitan angiosperm order that consists of four families: Leguminosae (Fabaceae), Polygalaceae, Surianaceae, and Quillajaceae. Despite the great interest in this group, a convincing phylogeny of the order is still not available. Therefore, the aim of this study was to explicitly test for possible long branch attraction (LBA) problems within Fabales for the first time, and determine whether low tree stemminess and unequal branch lengths could worsen this problem. Supermatrix analysis of Fabales was carried out using previously published plastid matK, trnL, rbcL, and newly sequenced nuclear sqd1 regions for 678 taxa in total, including 43 outgroup taxa from families of Fabidae. We employed additional analyses, such as simulations, network analyses, sampling different outgroup taxa (random or real), removing fast evolving sites and fast evolving taxa, and molecular clock rooting, to identify both LBA and (or) rooting problems. These analyses clearly show that the Fabales phylogeny has been influenced by the sampling of outgroup taxa, but not LBA. However, network analyses show that even though it is weak, there is a consistent phylogenetic signal among the rapidly radiated Fabales families, which can be traced by further analyses. While, molecular clock rooting analysis yielded a (Leguminosae(Polygalaceae(Surianaceae+Quillajaceae))) topology with strong support for the first time here, supermatrix analyses yielded a ((Leguminosae+Polygalaceae)(Surianaceae+Quillajaceae)) with low-moderate support.

scholarly journals Clinical significance of late diastolic tissue doppler parameters after onset of STEMI: from the view point of the timing of the echocardipography

2020 ◽  
Vol 41 (Supplement_2) ◽  
Author(s):  
N Iwahashi ◽  
J Kirigaya ◽  
M Horii ◽  
T Abe ◽  
E Akiyama ◽  
...  
Keyword(s):  
Tissue Doppler ◽  
Atrial Function ◽  
Diastolic Velocity ◽  
Long Time ◽  
Group A ◽  
St Elevation ◽  
Group B ◽  
First Time

Abstract Background The early transmitral flow velocity (E) divided by the early diastolic velocity of the mitral valve annulus (e') is referred to as the “E/e' ratio,” is useful even for ST elevation acute myocardial infarction (STEMI). However, the role of late diastolic velocity (a') which reveals the atrial function for STEMI is still unclear. Objectives We evaluated the clinical usefulness of tissue Doppler including atrial function for a first-time STEMI by long time follow up. Furthermore, we evaluated the meaning of each parameters by performing immediately after PCI or 2 weeks later. Methods We treated consecutive 571 first-time STEMI patients by immediate PCI within 12 hours after onset, and we examined 270 patients at immediately after PCI (GroupA, 65 years, 250 male) and 301 patients at 2 weeks after onset (GroupB, 64 years, 243 male). We examined trans mitral flow and TDI, then defined E/e' as LV filling pressure and A/a' as left atrial function. We followed them for a long time (>5 years). The primary end point (PE) was cardiac death or re-admission for heart failure (HF). Results We followed the patients in Group A for 10 years, Group B for 5 years. PE occurred in 64 patients in GroupA during 10 years, and 45 patients in GroupB during 5 years. We analyzed the univariate and multivariate Cox hazard analyses and we compared e' and a', E/e' and A/a' (Table). In GroupA, a' and A/a' were the independent predictors, on the other hand neither a' nor A/a' were the predictors in GroupB. E/e' was an independent predictor both in GroupA and B. Conclusion TDI parameters have different meanings by the timing of echocardiography after onset of a first-time STEMI. These results demonstrated that atrial dysfunction immediately after onset of STEMI suggests the poor prognosis after STEMI. Cox Hazard Proportional Analysis Funding Acknowledgement Type of funding source: None

scholarly journals Prevalence and Genetic Diversity of Group A Rotavirus Genotypes in Moscow (2019–2020)

Pathogens ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 674
Author(s):  
Anton Yuzhakov ◽  
Ksenia Yuzhakova ◽  
Nadezhda Kulikova ◽  
Lidia Kisteneva ◽  
Stanislav Cherepushkin ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Genetic Diversity ◽  
Acute Gastroenteritis ◽  
Rt Pcr ◽  
Clinical Hospital ◽  
Group A Rotavirus ◽  
Group A ◽  
First Time ◽  
Common Combination ◽  
Children Under 5

Group A rotavirus (RVA) infection is the leading cause of hospitalization of children under 5 years old, presenting with symptoms of acute gastroenteritis. The aim of our study was to explore the genetic diversity of RVA among patients admitted to Moscow Infectious Disease Clinical Hospital No. 1 with symptoms of acute gastroenteritis. A total of 653 samples were collected from May 2019 through March 2020. Out of them, 135 (20.67%) fecal samples were found to be positive for rotavirus antigen by ELISA. RT-PCR detected rotavirus RNA in 80 samples. Seven G-genotypes (G1, G2, G3, G4, G8, G9, and G12) and three P-genotypes (P[8], P[4], and P[6]) formed 9 different combinations. The most common combination was G9P[8]. However, for the first time in Moscow, the combination G3P[8] took second place. Moreover, all detected viruses of this combination belonged to Equine-like G3P[8] viruses that had never been detected in Russia before. The genotype G8P[8] and G9P[4] rotaviruses were also detected in Moscow for the first time. Among the studied rotaviruses, there were equal proportions of Wa and DS-1-like strains; previous studies showed that Wa-like strains accounted for the largest proportion of rotaviruses in Russia.

Study of the genus Meleonoma Meyrick, 1914 (Lepidoptera: Autostichidae) from China (III), with descriptions of eighteen new species

Zootaxa ◽  
2021 ◽  
Vol 4995 (2) ◽  
pp. 303-333
Author(s):  
SHUXIA WANG ◽  
XIAOJU ZHU ◽  
ZHULIN TAO
Keyword(s):  
New Species ◽  
Species Group ◽  
Group A ◽  
Species Groups ◽  
First Time

Eighteen new species of the genus Meleonoma Meyrick are described: M. arcivalvata sp. nov., M. chongqingensis sp. nov., M. curvativa sp. nov., M. curvitaeniana sp. nov., M. dilatifasciata sp. nov., M. fasciptera sp. nov., M. globoidea sp. nov., M. graciliclavata sp. nov., M. grandivalvula sp. nov., M. lunata sp. nov., M. medispinea sp. nov., M. proapicalis sp. nov., M. raphidacantha sp. nov., M. sinuaclavata sp. nov., M. tenuiclavata sp. nov., M. tetrodonta sp. nov. M. ventridentata sp. nov. and M. ventrisinuata sp. nov. The female of M. similifloralis (Wang, 2006) is described for the first time. Images of both adults and genitalia are provided. All species are divided into two species-groups, the dentivalvata species-group and the fasciptera species-group. A key to each group and maps showing the distribution of each group in China are given.  

A phylogenetic revision of Calydna and relatives (Lepidoptera: Riodinidae)

2002 ◽  
Vol 33 (2) ◽  
pp. 185-237 ◽  
Author(s):  
Jason P.W. Hall
Keyword(s):  
Phylogenetic Analysis ◽  
New Genus ◽  
Male And Female ◽  
Basal Clade ◽  
Two New Species ◽  
Group A ◽  
Species Groups ◽  
First Time ◽  
The Relationship ◽  
Phylogenetic Revision

AbstractA phylogenetic revision of the Neotropical riodinid genus Calydna Doubleday and relatives is presented. A phylogenetic analysis for all twenty species of Calydna using thirty-eight characters of adult morphology generated four most parsimonious cladograms. Calydna is characterised to contain eighteen species, divided here into three monophyletic species groups with the relationship caieta group + (thersander group + hiria group). A new genus Echydna Hall gen. n. is described for the most basal clade, containing chaseba Hewitson and punctata C. & R. Felder, which are transferred from Calydna (combs. n.). The taxonomy, morphology, biogeography and biology of both genera are discussed, locality data is listed and mapped, and the adults and male and female genitalia are illustrated for all species. Concealed male abdominal androconial scales, which phylogenetically unite the thersander and hiria groups, are reported for the first time outside of the tribes Symmachiini and Nymphidiini. Two new species are described, Calydna jeannea sp. n. and Calydna nicolayi sp. n., and the replacement name fissilisima is provided for the unavailable name fissilis Stichel; maculosa Bates is transferred from Calydna to Callistium Stichel (comb. n.).

Taxonomic re-evaluation of the monotypic genus Pararhabdophis Bourret, 1934 (Squamata: Colubridae: Natricinae) with discovery of its type species, P. chapaensis, from China

Zootaxa ◽  
2018 ◽  
Vol 4486 (1) ◽  
pp. 31
Author(s):  
JIN-LONG REN ◽  
KAI WANG ◽  
TAO THIEN NGUYEN ◽  
CHUNG VAN HOANG ◽  
GUANG-HUI ZHONG ◽  
...  
Keyword(s):  
Natural History ◽  
Type Species ◽  
Yunnan Province ◽  
Strong Support ◽  
Taxonomic Position ◽  
Monotypic Genus ◽  
History Data ◽  
Lao Cai ◽  
Available Information ◽  
First Time

The Asian monotypic genus Pararhabdophis Bourret, 1934 has long been known from a single holotype of the type species Pararhabdophis chapaensis Bourret, 1934 only. The limited available information hampered the identification of the natricine species. On the basis of eight newly collected specimens of P. chapaensis from the type locality in Sa Pa, Lao Cai Province, Vietnam and from Pingbian, Yunnan Province in southwestern China, the taxonomic position of the genus Pararhabdophis was re-evaluated using both morphological and molecular datasets for the first time. Pararhabdophis chapaensis is nested within the genus Hebius Thompson, 1913 with strong support, and morphologically indistinguishable from the latter genus. As a consequence, we herein synonymize the genus Pararhabdophis with Hebius and discuss about the existing paraphyly of some Hebius species. In addition we report Hebius chapaensis for the first time from China and provide redescription and natural history data of this poorly known species. To facilitate future taxonomic work, an identification key to all known natricine genera from China and Vietnam is also provided. 

Phylogeny of the Styracaceae Revisited Based on Whole Plastome Sequences, Including Novel Plastome Data from Parastyrax

2021 ◽  
Vol 46 (1) ◽  
pp. 162-174
Author(s):  
Ming-Hui Yan ◽  
Chun-Yang Li ◽  
Peter W. Fritsch ◽  
Jie Cai ◽  
Heng-Chang Wang
Keyword(s):  
Phylogenetic Relationships ◽  
Phylogenetic Signal ◽  
Strong Support ◽  
Single Copy ◽  
Rrna Genes ◽  
Trna Genes ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
The Family ◽  
Small Single Copy

Abstract—The phylogenetic relationships among 11 out of the 12 genera of the angiosperm family Styracaceae have been largely resolved with DNA sequence data based on all protein-coding genes of the plastome. The only genus that has not been phylogenomically investigated in the family with molecular data is the monotypic genus Parastyrax, which is extremely rare in the wild and difficult to collect. To complete the sampling of the genera comprising the Styracaceae, examine the plastome composition of Parastyrax, and further explore the phylogenetic relationships of the entire family, we sequenced the whole plastome of P. lacei and incorporated it into the Styracaceae dataset for phylogenetic analysis. Similar to most others in the family, the plastome is 158189 bp in length and contains a large single-copy region of 88085 bp and a small single-copy region of 18540 bp separated by two inverted-repeat regions of 25781 bp each. A total of 113 genes was predicted, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic relationships among all 12 genera of the family were constructed with 79 protein-coding genes. Consistent with a previous study, Styrax, Huodendron, and a clade of Alniphyllum + Bruinsmia were successively sister to the remainder of the family. Parastyrax was strongly supported as sister to an internal clade comprising seven other genera of the family, whereas Halesia and Pterostyrax were both recovered as polyphyletic, as in prior studies. However, when we employed either the whole plastome or the large- or small-single copy regions as datasets, Pterostyrax was resolved as monophyletic with 100% support, consistent with expectations based on morphology and indicating that non-coding regions of the Styracaceae plastome contain informative phylogenetic signal. Conversely Halesia was still resolved as polyphyletic but with novel strong support.

Effects of spaceflight on rat erythroid parameters

1996 ◽  
Vol 81 (1) ◽  
pp. 117-122 ◽  
Author(s):  
Z. Allebban ◽  
L. A. Gibson ◽  
R. D. Lange ◽  
T. L. Jago ◽  
K. M. Strickland ◽  
...  
Keyword(s):  
Bone Marrow ◽  
Life Sciences ◽  
Lower Number ◽  
Ground Control ◽  
Colony Forming Unit ◽  
Human Erythropoietin ◽  
Group A ◽  
Group B ◽  
First Time ◽  
Group D

Hematologic studies were performed on 21 ground control rats and 21 rats flown during the Spacelab Life Sciences-2 14-day mission. Group A (n = 5) was used to collect blood in flight and 9 days postflight, group B (n = 5) was injected with recombinant human erythropoietin (rhEpo), group C (n = 5) received saline as a control, and group D (n = 6) was killed in flight and tissues were collected. Results indicated no significant changes in peripheral blood erythroid elements between flight and ground control rats. The nonadherent bone marrow on flight day 13 showed a lower number of recombinant rat interleukin-3 (rrIL-3)-responsive and rrIL-3 + rhEpo-responsive blast-forming unit erythroid (BFU-e) colonies in flight rats compared with ground control rats. On landing day, a slight increase in the number of rhEpo + rrIL-3-responsive BFU-e colonies of flight animals compared with ground control rats was evident. Nine days postflight, bone marrow from flight rats stimulated with rhEpo alone or with rhEpo + rrIL-3 showed an increase in the number of colony-forming unit erythroid colonies and a decrease in BFU-e colonies compared with ground control rats. This is the first time that animals were injected with rhEpo and subsequently blood and tissues were collected during the spaceflight to study the regulation of erythropoiesis in microgravity.

scholarly journals Clock-Controlled Mitochondrial Dynamics Correlates with Cyclic Pregnenolone Synthesis

Cells ◽  
2020 ◽  
Vol 9 (10) ◽  
pp. 2323
Author(s):  
Melissa Witzig ◽  
Amandine Grimm ◽  
Karen Schmitt ◽  
Imane Lejri ◽  
Stephan Frank ◽  
...  
Keyword(s):  
Molecular Clock ◽  
Mitochondrial Dynamics ◽  
Glioma Cells ◽  
Translocator Protein ◽  
Mitochondrial Morphology ◽  
Circadian Regulation ◽  
The Core ◽  
Steroidogenic Cells ◽  
First Time ◽  
A172 Glioma Cells

Neurosteroids are steroids synthetized in the nervous system, with the first step of steroidogenesis taking place within mitochondria with the synthesis of pregnenolone. They exert important brain-specific functions by playing a role in neurotransmission, learning and memory processes, and neuroprotection. Here, we show for the first time that mitochondrial neurosteroidogenesis follows a circadian rhythm and correlates with the rhythmic changes in mitochondrial morphology. We used synchronized human A172 glioma cells, which are steroidogenic cells with a functional core molecular clock, to show that pregnenolone levels and translocator protein (TSPO) are controlled by the clock, probably via circadian regulation of mitochondrial fusion/fission. Key findings were recapitulated in mouse brains. We also showed that genetic or pharmacological abrogation of fusion/fission activity, as well as disturbing the core molecular clock, abolished circadian rhythms of pregnenolone and TSPO. Our findings provide new insights into the crosstalk between mitochondrial function (here, neurosteroidogenesis) and circadian cycles.

Feather morphological predictors of angle-dependent color changes in parrot plumage

2020 ◽  
Vol 13 (4) ◽  
pp. 108-117
Author(s):  
Steven Reed ◽  
Richard K Simpson ◽  
Kevin J McGraw
Keyword(s):  
Phylogenetic Signal ◽  
Interspecific Variation ◽  
Plumage Color ◽  
Color Changes ◽  
Structural Colors ◽  
Angle Dependence ◽  
Novel Approach ◽  
Euclidean Distances ◽  
Parrot Species ◽  
First Time

Among the most ornate animal traits in nature are the angle-dependent (e.g. iridescent) structural colors of many fishes, damselflies, birds, beetles, and butterflies. Though we now have a solid understanding of the mechanisms that create angle-dependent coloration in several groups, we know little about whether pigmentary colors reflect light in an angle-dependent fashion or if similar or different mechanisms govern angle-dependent reflectance from pigmentary versus structural colors. Here for the first time we describe non-iridescent angle-dependent coloration from the tail and wing feathers of several parrot species (Aves: Psittaciformes). We employed a novel approach—by calculating chromatic and achromatic contrasts (in just noticeable differences, JNDs) of straight and angled measurements of the same feather patch—to test for perceptually relevant angle-dependent changes in coloration on dorsal and ventral feather surfaces. We found, among the 15 parrot species studied, significant angle dependence for seven of our eight feather JND parameters. We then measured micro-scale features on each side of feathers, including size and color of barbs and barbules, to attempt to predict interspecific variation in degree of angle-dependent reflectance. We found that barb height, plumage-color type (e.g. melanin, structural), and differences between barb-barbule coloration (measured using Euclidean distances) were the strongest predictors of angle-dependent coloration. Interestingly, there was no significant phylogenetic signal in any of the angle-dependence models tested. These findings deepen our views on the importance of microscopic feather features in the production of directional animal coloration, especially in tissues that are colored predominantly by pigments and appear to be statically colored.

scholarly journals Molecular Epidemiology of Rotavirus A Strains Pre- and Post-Vaccine (Rotarix®) Introduction in Mozambique, 2012–2019: Emergence of Genotypes G3P[4] and G3P[8]

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 671 ◽  
Author(s):  
Eva D. João ◽  
Benilde Munlela ◽  
Assucênio Chissaque ◽  
Jorfélia Chilaúle ◽  
Jerónimo Langa ◽  
...  
Keyword(s):  
Acute Diarrhea ◽  
Sentinel Site ◽  
Predominant Genotype ◽  
Post Vaccination ◽  
Rotavirus A ◽  
Strain Diversity ◽  
Monovalent Vaccine ◽  
Group A ◽  
Expanded Program On Immunization ◽  
First Time

Group A rotavirus (RVA) remains the most important etiological agent associated with severe acute diarrhea in children. Rotarix® monovalent vaccine was introduced into Mozambique’s Expanded Program on Immunization in September 2015. In the present study, we report the diversity and prevalence of rotavirus genotypes, pre- (2012–2015) and post-vaccine (2016–2019) introduction in Mozambique, among diarrheic children less than five years of age. Genotyping data were analyzed for five sentinel sites for the periods indicated. The primary sentinel site, Mavalane General Hospital (HGM), was analyzed for the period 2012–2019, and for all five sites (country-wide analyses), 2015–2019. During the pre-vaccine period, G9P[8] was the most predominant genotype for both HGM (28.5%) and the country-wide analysis (46.0%). However, in the post-vaccine period, G9P[8] was significantly reduced. Instead, G3P[8] was the most common genotype at HGM, while G1P[8] predominated country-wide. Genotypes G9P[4] and G9P[6] were detected for the first time, and the emergence of G3P[8] and G3P[4] genotypes were observed during the post-vaccine period. The distribution and prevalence of rotavirus genotypes were distinct in pre- and post-vaccination periods, while uncommon genotypes were also detected in the post-vaccine period. These observations support the need for continued country-wide surveillance to monitor changes in strain diversity, due to possible vaccine pressure, and consequently, the effect on vaccine effectiveness.

Sign in / Sign up

Export Citation Format

Share Document