Reliable Identification of Environmental Fungi Requires Multigene-Based Phylogenetic Analyses

Diseases caused by phytoplasmas have been reported in field crops, ornamentals, and weeds in Indonesia. However, most of phytoplasmas have not been subjected to further identification and thus, they remain unaffiliated with proper classification scheme. More reliable identification of phytoplasmas mostly rely on molecular methods. The aim of this study was to characterize the phytoplasma as the causal agent of naturally infected plants in western Java-Indonesia based on their 16S rRNA nucleotide sequences. Plant exhibiting phytoplasmal symptoms were observed and taken for further molecular examination. Eight plant species from three families in Bogor, Tangerang, and Bekasi, i.e. peanut, soybean, snakebean, Opuntia sp., betung bamboo, apus bamboo, Bermuda grass, and digitaria grass (Digitaria fuscescens) have been observed and taken as samples for further molecular examination. Nested-PCR with primer pairs P1/P7 followed by R16F2n/R16R2 resulted in amplification of products of approximately 1.2 kb from all symptomatic plant samples tested. BLAST analysis of the nucleotide sequences, phylogenetic analyses, and similarity coefficients derived from RFLP in silico revealed that there were association of a phytoplasma of 16SrII-A subgroup with phytoplasmas identified in peanut, soybean, and snakebean. Such an association showed witches’ broom symptoms; 16SrII-C with Opuntia sp. causing proliferation and mosaics; and phytoplasmas displaying yellowing and little leaf of two kinds of bamboos and white leaf of Bermuda grass and digitaria grass that were closely related to 16SrXIV-A subgroup. To our knowledge, this is the first report molecular identification of 16SrXIV-A associated with apus bamboo and digitaria grass in Indonesia.

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Ellipsomyxa ariusi sp. nov. (Myxosporea: Ceratomyxidae), a new myxosporean infecting the gallbladder of threadfin sea catfish Arius arius in India

Diseases of Aquatic Organisms ◽

10.3354/dao03529 ◽

2020 ◽

Vol 142 ◽

pp. 83-97

Author(s):

A Chandran ◽

PU Zacharia ◽

TV Sathianandan ◽

NK Sanil

Keyword(s):

Phylogenetic Analyses ◽

Type Specimen ◽

Ssu Rdna ◽

Fish Host ◽

Present Species ◽

Epithelial Layer ◽

Histopathological Changes ◽

Mucus Production ◽

High Bootstrap ◽

A New Species

The present study describes a new species of myxosporean, Ellipsomyxa ariusi sp. nov., infecting the gallbladder of the threadfin sea catfish Arius arius (Hamilton, 1822). E. ariusi sp. nov. is characterized by bivalvular, ellipsoid or elongate-oval myxospores with smooth spore valves and a straight suture, arranged at an angle to the longitudinal spore axis. Mature myxospores measured 10.1 ± 0.8 µm in length, 6.8 ± 0.5 µm in width and 7.7 ± 0.7 µm in thickness. Polar capsules are equal in size and oval to pyriform in shape. They are positioned at an angle to the longitudinal myxospore axis and open in opposite directions. Polar capsules measured 2.8 ± 0.3 µm in length and 2.5 ± 0.4 µm in width; polar filaments formed 4-5 coils, and extended to 32.2 ± 2.1 µm in length. Monosporic and disporic plasmodial stages attached to the wall of gallbladder. Molecular analysis of the type specimen generated a 1703 bp partial SSU rDNA sequence (MN892546), which was identical to the isolates from 3 other locations. In phylogenetic analyses, genus Ellipsomyxa appeared monophyletic and E. ariusi sp. nov. occupied an independent position in maximum likelihood and Bayesian inference trees with high bootstrap values. The overall prevalence of infection was 54.8% and multiway ANOVA revealed that it varied significantly with location, year, season, sex and size of the fish host. Histopathological changes associated with E. ariusi sp. nov. infection included swelling, vacuolation and detachment of epithelial layer, reduced mucus production and altered consistency and colour of bile. Based on the morphologic, morphometric and molecular differences with known species of Ellipsomyxa, and considering differences in host and geographic locations, the present species is treated as new and the name Ellipsomyxa ariusi sp. nov. is proposed.

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Diversification of the North American Doellingeria-Eucephalus Clade (Astereae: Asteraceae) Inferred from Molecular and Morphological Evidence

Systematic Botany ◽

10.1600/036364419x15710776741477 ◽

2019 ◽

Vol 44 (4) ◽

pp. 930-942

Author(s):

Geraldine A. Allen ◽

Luc Brouillet ◽

John C. Semple ◽

Heidi J. Guest ◽

Robert Underhill

Keyword(s):

North American ◽

Sequence Data ◽

Phylogenetic Analyses ◽

Sister Group ◽

Morphological Evidence ◽

South American ◽

New Combinations ◽

The North ◽

Hybridization Event ◽

Ancient Hybridization

Abstract—Doellingeria and Eucephalus form the earliest-diverging clade of the North American Astereae lineage. Phylogenetic analyses of both nuclear and plastid sequence data show that the Doellingeria-Eucephalus clade consists of two main subclades that differ from current circumscriptions of the two genera. Doellingeria is the sister group to E. elegans, and the Doellingeria + E. elegans subclade in turn is sister to the subclade containing all remaining species of Eucephalus. In the plastid phylogeny, the two subclades are deeply divergent, a pattern that is consistent with an ancient hybridization event involving ancestral species of the Doellingeria-Eucephalus clade and an ancestral taxon of a related North American or South American group. Divergence of the two Doellingeria-Eucephalus subclades may have occurred in association with northward migration from South American ancestors. We combine these two genera under the older of the two names, Doellingeria, and propose 12 new combinations (10 species and two varieties) for all species of Eucephalus.

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Cultural evolution and cultural psychology

10.31234/osf.io/7k86h ◽

2018 ◽

Author(s):

Alex Mesoudi

Keyword(s):

Cultural History ◽

Cultural Evolution ◽

Cultural Transmission ◽

Cultural Psychology ◽

Phylogenetic Analyses ◽

Cultural Dimensions ◽

Human Cognition ◽

Cultural Variation ◽

Cultural Inheritance ◽

Human Psychology

Cultural evolution is a branch of the evolutionary sciences which assumes that (i) human cognition and behaviour is shaped not only by genetic inheritance, but also cultural inheritance (also known as social learning), and (ii) this cultural inheritance constitutes a Darwinian evolutionary system that can be analysed and studied using tools borrowed from evolutionary biology. In this chapter I explore the numerous compatibilities between the fields of cultural evolution and cultural psychology, and the potential mutual benefits from their closer alignment. First, understanding the evolutionary context within which human psychology emerged gives added significance to the findings of cultural psychologists, which reinforce the conclusion reached by cultural evolution scholars that humans inhabit a ‘cultural niche’ within which the major means of adaptation to difference environments is cultural, rather than genetic. Hence, we should not be surprised that human psychology shows substantial cross-cultural variation. Second, a focus on cultural transmission pathways, drawing on cultural evolution models and empirical research, can help to explain to the maintenance of, and potential changes in, cultural variation in psychological processes. Evidence from migrants, in particular, points to a mix of vertical, oblique and horizontal cultural transmission that can explain the differential stability of different cultural dimensions. Third, cultural evolutionary methods offer powerful means of testing historical (“macro-evolutionary”) hypotheses put forward by cultural psychologists for the origin of psychological differences. Explanations in terms of means of subsistence, rates of environmental change or pathogen prevalence can be tested using quantitative models and phylogenetic analyses that can be used to reconstruct cultural lineages. Evolutionary considerations also point to potential problems with current cross-country comparisons conducted within cultural psychology, such as the non-independence of data points due to shared cultural history. Finally, I argue that cultural psychology can play a central role in a synthetic evolutionary science of culture, providing valuable links between individual-oriented disciplines such as experimental psychology and neuroscience on the one hand, and society-oriented disciplines such as anthropology, history and sociology on the other, all within an evolutionary framework that provides links to the biological sciences.

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Faculty Opinions recommendation of Inter- and intraspecies phylogenetic analyses reveal extensive X-Y gene conversion in the evolution of gametologous sequences of human sex chromosomes.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.718382559.793497569 ◽

2014 ◽

Author(s):

Deborah Charlesworth

Keyword(s):

Gene Conversion ◽

Sex Chromosomes ◽

Phylogenetic Analyses

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Genetic Diversity and Drug Resistance of HIV-1 CRF55_01B in Guangdong, China

Current HIV Research ◽

10.2174/1570162x18666200415140652 ◽

2020 ◽

Vol 18 (3) ◽

pp. 210-218

Author(s):

Guolong Yu ◽

Yan Li ◽

Xuhe Huang ◽

Pingping Zhou ◽

Jin Yan ◽

...

Keyword(s):

Genetic Diversity ◽

Drug Resistance ◽

Reverse Transcriptase ◽

Phylogenetic Analyses ◽

Resistance Mutations ◽

Protease Inhibition ◽

Subtype B ◽

Primary Drug Resistance ◽

Hiv 1 ◽

Primary Drug

Background: HIV-1 CRF55_01B was first reported in 2013. At present, no report is available regarding this new clade’s polymorphisms in its functionally critical regions protease and reverse transcriptase. Objective: To identify the diversity difference in protease and reverse transcriptase between CRF55_01B and its parental clades CRF01_AE and subtype B; and to investigate CRF55_01B’s drug resistance mutations associated with the protease inhibition and reverse transcriptase inhibition. Methods: HIV-1 RNA was extracted from plasma derived from a MSM population. The reverse transcription and nested PCR amplification were performed following our in-house PCR procedure. Genotyping and drug resistant-associated mutations and polymorphisms were identified based on polygenetic analyses and the usage of the HIV Drug Resistance Database, respectively. Results: A total of 9.24 % of the identified CRF55_01B sequences bear the primary drug resistance. CRF55_01B contains polymorphisms I13I/V, G16E and E35D that differ from those in CRF01_AE. Among the 11 polymorphisms in the RT region, seven were statistically different from CRF01_AE’s. Another three polymorphisms, R211K (98.3%), F214L (98.3%), and V245A/E (98.3 %.), were identified in the RT region and they all were statistically different with that of the subtype B. The V179E/D mutation, responsible for 100% potential low-level drug resistance, was found in all CRF55_01B sequences. Lastly, the phylogenetic analyses demonstrated 18 distinct clusters that account for 35% of the samples. Conclusions: CRF55_01B’s pol has different genetic diversity comparing to its counterpart in CRF55_01B’s parental clades. CRF55_01B has a high primary drug resistance presence and the V179E/D mutation may confer more vulnerability to drug resistance.

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The Frequency of HIV-1 Infection in Iranian Children and Determination of the Transmitted Drug Resistance in Treatment-Naïve Children

Current HIV Research ◽

10.2174/1570162x17666191106111211 ◽

2020 ◽

Vol 17 (6) ◽

pp. 397-407

Author(s):

Maryam Jarchi ◽

Farah Bokharaei-Salim ◽

Maryam Esghaei ◽

Seyed Jalal Kiani ◽

Fatemeh Jahanbakhsh ◽

...

Keyword(s):

Drug Resistance ◽

Pediatric Patients ◽

Phylogenetic Analyses ◽

Rna Extraction ◽

Transmitted Drug Resistance ◽

The Arts ◽

Treatment Naïve ◽

Iranian Children ◽

Hiv 1

Background: The advent of resistance-associated mutations in HIV-1 is a barrier to the success of the ARTs. Objective: In this study, the abundance of HIV-1 infection in Iranian children, and also detection of the TDR in naïve HIV-1 infected pediatric (under 12 years old) were evaluated. Materials: From June 2014 to January 2019, a total of 544 consecutive treatment-naïve HIV-1- infected individuals enrolled in this study. After RNA extraction, amplification, and sequencing of the HIV-1 pol gene, the DRM and phylogenetic analysis were successfully performed on the plasma specimens of the ART-naïve HIV-1-infected-children under 12 years old. The DRMs were recognized using the Stanford HIV Drug Resistance Database. Results: Out of the 544 evaluated treatment-naïve HIV-1-infected individuals, 15 (2.8%) cases were children under 12 years old. The phylogenetic analyses of the amplified region of pol gene indicated that all of the 15 HIV-1-infected pediatric patients were infected by CRF35_AD, and a total of 13.3% (2/15) of these children were infected with HIV-1 variants with SDRMs (one child harbored two related SDRMs [D67N, V179F], and another child had three related SDRMs [M184V, T215F, and K103N]), according to the last algorithm of the WHO. No PIs-related SDRMs were observed in HIV-1-infected children. Conclusion: The current study demonstrated that a total of 13.3% of treatment-naïve HIV-1-infected Iranian pediatrics (under 12 years old) were infected with HIV-1 variants with SDRMs. Therefore, it seems that screening to recognize resistance-associated mutations before the initiation of ARTs among Iranian children is essential for favorable medication efficacy and dependable prognosis.

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African Origin of Human T-Lymphotropic Virus Type 2 (HTLV-2) Supported by a Potential New HTLV-2d Subtype in Congolese Bambuti Efe Pygmies

Journal of Virology ◽

10.1128/jvi.72.5.4327-4340.1998 ◽

1998 ◽

Vol 72 (5) ◽

pp. 4327-4340 ◽

Cited By ~ 49

Author(s):

Anne-Mieke Vandamme ◽

Marco Salemi ◽

Marianne Van Brussel ◽

Hsin-Fu Liu ◽

Kristel Van Laethem ◽

...

Keyword(s):

T Cell ◽

Virus Type ◽

Phylogenetic Analyses ◽

Enzyme Linked Immunosorbent Assay ◽

African Origin ◽

Entire Genome ◽

T Lymphotropic Virus ◽

Tax Protein ◽

Human T Cell

ABSTRACT We identified a potential new subtype within human T-cell lymphotropic virus type 2 (HTLV-2), HTLV-2d, present in members of an isolated Efe Bambuti Pygmy tribe. Two of 23 Efe Pygmies were HTLV-2 seropositive, with HTLV-2 Western blot and enzyme-linked immunosorbent assay reactivities. From one of them the entire genome of the HTLV-2 strain Efe2 could be amplified and sequenced. In all gene regions analyzed, this strain was the most divergent HTLV-2 strain, differing by 2.4% (tax/rex) to 10.7% (long terminal repeat) from both subtypes HTLV-2a and HTLV-2b, yet major functional elements are conserved. The similarity between the HTLV-2 Efe2 Gag and Env proteins and the corresponding HTLV-2a and -2b proteins is consistent with the observed serological reactivity. In the proximal pX region, one of the two alternative splice acceptor sites is abolished in HTLV-2 Efe2. Another interesting feature of this potential new subtype is that it has a Tax protein of 344 amino acids (aa), which is intermediate in length between the HTLV-2a Tax protein (331 aa) and the HTLV-2b and -2c Tax proteins (356 aa) and similar to the simian T-cell lymphotropic virus type 2 (STLV-2) PP1664 Tax protein. Together these two findings suggest a different phenotype for the HTLV-2 Efe2 strain. Phylogenetic analyses confirmed that the Pygmy Efe2 strain potentially belonged to a new and quite divergent subtype, HTLV-2d. When the STLV-2 bonobo viruses PP1664 and PanP were used as an outgroup, it was clear that the Pygmy HTLV-2 Efe2 strain had the longest independent evolution and that HTLV-2 evolution is consistent with an African origin.

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Dealing with Normatively Inappropriate Dissent

10.1093/oso/9780190869229.003.0006 ◽

2018 ◽

Author(s):

Inmaculada de Melo-Martín ◽

Kristen Intemann

Keyword(s):

Social Impacts ◽

Reliable Identification ◽

Public Beliefs ◽

Negative Impacts ◽

Epistemic Obligations

This chapter considers whether the reliable identification of normatively inappropriate dissent (NID) would be helpful in addressing many of the adverse epistemic and social impacts that can result from it. It considers a variety of ways in which such identification could be used to minimize the epistemic and social damages that NID can inflict, including prohibiting the dissent in question, targeting it for special scrutiny, placing limits on scientists’ epistemic obligations, guiding public beliefs, emphasizing the existence of a consensus, and discrediting dissenters. It shows that although some of these strategies could be useful, others are unhelpful in limiting the negative impacts of NID, and may even exacerbate them or generate other equally serious problems.

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Telomere length varies substantially between blood cell types in a reptile

Royal Society Open Science ◽

10.1098/rsos.192136 ◽

2020 ◽

Vol 7 (6) ◽

pp. 192136 ◽

Cited By ~ 3

Author(s):

Mats Olsson ◽

Nicholas J. Geraghty ◽

Erik Wapstra ◽

Mark Wilson

Keyword(s):

Blood Cell ◽

Telomere Length ◽

Whole Blood ◽

Phylogenetic Analyses ◽

Natural Populations ◽

Cell Types ◽

Tissue Type ◽

Telomeric Dna ◽

Blood Cell Type ◽

Widespread Phenomenon

Telomeres are repeat sequences of non-coding DNA-protein molecules that cap or intersperse metazoan chromosomes. Interest in telomeres has increased exponentially in recent years, to now include their ongoing dynamics and evolution within natural populations where individuals vary in telomere attributes. Phylogenetic analyses show profound differences in telomere length across non-model taxa. However, telomeres may also differ in length within individuals and between tissues. The latter becomes a potential source of error when researchers use different tissues for extracting DNA for telomere analysis and scientific inference. A commonly used tissue type for assessing telomere length is blood, a tissue that itself varies in terms of nuclear content among taxa, in particular to what degree their thrombocytes and red blood cells (RBCs) contain nuclei or not. Specifically, when RBCs lack nuclei, leucocytes become the main source of telomeric DNA. RBCs and leucocytes differ in lifespan and how long they have been exposed to ‘senescence' and erosion effects. We report on a study in which cells in whole blood from individual Australian painted dragon lizards ( Ctenophorus pictus ) were identified using flow cytometry and their telomere length simultaneously measured. Lymphocyte telomeres were on average 270% longer than RBC telomeres, and in azurophils (a reptilian monocyte), telomeres were more than 388% longer than those in RBCs. If this variation in telomere length among different blood cell types is a widespread phenomenon, and DNA for comparative telomere analyses are sourced from whole blood, evolutionary inference of telomere traits among taxa may be seriously complicated by the blood cell type comprising the main source of DNA.

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