scholarly journals Repeated duplication of Argonaute2 is associated with strong selection and testis specialization in Drosophila

2016 ◽  
Author(s):  
Samuel H. Lewis ◽  
Claire L. Webster ◽  
Heli Salmela ◽  
Darren J. Obbard
Keyword(s):  
Transposable Elements ◽  
Species Group ◽  
Gene Copy ◽  
Rnai Pathway ◽  
Specific Expression ◽  
Strong Selection ◽  
Use Patterns ◽  
Link Type ◽  
Syntenic Gene ◽  
History Of

AbstractArgonaute2 (Ago2) is a rapidly evolving nuclease in the Drosophila melanogaster RNA interference (RNAi) pathway that targets viruses and transposable elements in somatic tissues. Here we reconstruct the history of Ago2 duplications across the Drosophila obscura group, and use patterns of gene expression to infer new functional specialization. We show that some duplications are old, shared by the entire species group, and that losses may be common, including previously undetected losses in the lineage leading to D. pseudoobscura. We find that while the original (syntenic) gene copy has generally retained the ancestral ubiquitous expression pattern, most of the novel Ago2 paralogues have independently specialized to testis-specific expression. Using population genetic analyses, we show that most testis-specific paralogues have significantly lower genetic diversity than the genome-wide average. This suggests recent positive selection in three different species, and model-based analyses provide strong evidence of recent hard selective sweeps in or near four of the six D. pseudoobscura Ago2 paralogues. We speculate that the repeated evolution of testis-specificity in obscura group Ago2 genes, combined with their dynamic turnover and strong signatures of adaptive evolution, may be associated with highly derived roles in the suppression of transposable elements or meiotic drive. Our study highlights the lability of RNAi pathways, even within well-studied groups such as Drosophila, and suggests that strong selection may act quickly after duplication in RNAi pathways, potentially giving rise to new and unknown RNAi functions in non-model species.Supporting DataAll new sequences produced in this study have been submitted to Genbank as KX016642-KX016771.

scholarly journals Widespread gene duplication and adaptive evolution in the RNA interference pathways of the Drosophila obscura group

2018 ◽  
Author(s):  
Danang Crysnanto ◽  
Darren Obbard
Keyword(s):  
Rna Interference ◽  
Gene Duplication ◽  
Species Group ◽  
Rnai Pathway ◽  
Specific Expression ◽  
Argonaute 2 ◽  
History Of ◽  
Male Specific ◽  
Obscura Group ◽  
Adaptive Substitution

Background: RNA interference (RNAi) related pathways provide defense against viruses and transposable elements, and have been implicated in the suppression of meiotic drive elements. Genes in these pathways often exhibit high levels of adaptive substitution, and over longer timescales show gene duplication and los--most likely as a consequence of their role in mediating conflict with these parasites. This is particularly striking for Argonaute 2 (Ago2), which is ancestrally the key effector of antiviral RNAi in insects, but has repeatedly formed new testis-specific duplicates in the recent history of the obscura species-group of Drosophila. Results: Here we take advantage of publicly available genomic and transcriptomic data to identify six further RNAi-pathway genes that have duplicated in this clade of Drosophila, and examine their evolutionary history. As seen for Ago2, we observe high levels of adaptive amino-acid substitution and changes in sex-biased expression in many of the paralogs. However, our phylogenetic analysis suggests that co-duplications of the RNAi machinery were not synchronous, and our expression analysis fails to identify consistent male-specific expression. Conclusions: These results confirm that RNAi genes, including genes of the antiviral and piRNA pathways, have undergone multiple independent duplications and that their history has been particularly labile within the obscura group. However, they also suggest that the selective pressures driving these changes have not been consistent, implying that more than one selective agent may be responsible.

Identity of the oribatid mite Oribata curva and transfer to Trichogalumna (Acari, Oribatida, Galumnidae), with discussion of nomenclatural and biogeographical issues in the ‘curva’ species-group

Zootaxa ◽  
2017 ◽  
Vol 4272 (4) ◽  
pp. 551
Author(s):  
ROY A. NORTON ◽  
SERGEY G. ERMILOV
Keyword(s):  
North America ◽  
Oribatid Mite ◽  
Species Group ◽  
Type Material ◽  
Similar Species ◽  
History Of ◽  
Molecular Assessment

Based on the study of type material, other historical specimens, and new collections, the adult of the thelytokous oribatid mite Oribata curva Ewing, 1907 (Galumnidae) is redescribed and the name is recombined to Trichogalumna curva (Ewing, 1907) comb. nov. A confusing history of synonymies and misidentifications is traced in detail, and their effect on published statements about biogeography is assessed. Reliable records of T. curva are only those from North America. The tropical mite Pergalumna ventralis (Willmann, 1932) is not a subspecies of T. curva. The widely-reported Trichogalumna nipponica (Aoki, 1966) and other similar species form a complex with T. curva that needs further morphological and molecular assessment. 

Beyond Wallace: a new lineage of Chrysorthenches (Lepidoptera: Yponomeutoidea: Glyphipterigidae) reveals a journey tracking its host-plants, Podocarpus (Pinopsida: Podocarpaceae)

2020 ◽  
Vol 190 (2) ◽  
pp. 709-736
Author(s):  
Jae-Cheon Sohn ◽  
Shigeki Kobayashi ◽  
Yutaka Yoshiyasu
Keyword(s):  
Maximum Likelihood ◽  
East Asia ◽  
Host Plants ◽  
Morphological Characters ◽  
Species Group ◽  
Geological History ◽  
Dna Barcodes ◽  
History Of ◽  
Species Groups ◽  
Maximum Likelihood Phylogeny

Abstract A northward trans-Wallacean radiation is demonstrated for Chrysorthenches, a member of the Orthenches group. Here we review Chrysorthenches and allied genera resulting in a generic transfer of Diathryptica callibrya to Chrysorthenches and two new congeners: C. muraseaeSohn & Kobayashisp. nov. from Japan and C. smaragdinaSohnsp. nov. from Thailand. We review morphological characters of Chrysorthenches and allied genera, and find polyphyly of Diathryptica and the association of the Orthenches-group with Glyphipterigidae. These findings were supported in a maximum likelihood phylogeny of DNA barcodes from ten yponomeutoids. We analysed 30 morphological characters for 12 species of Chrysorthenches, plus one outgroup, via a cladistic approach. The resulting cladogram redefined two pre-existing Chrysorthenches species-groups and identified one novel lineage: the C. callibrya species-group. We review the host associations between Chrysorthenches and Podocarpaceae, based on mapping the working phylogenies. Our review suggests that ancestral Chrysorthenches colonized Podocarpus and later shifted to other podocarp genera. Biogeographical patterns of Chrysorthenches show that they evolved long after the Podocarpaceae radiation. Disjunctive trans-Wallacean distribution of the C. callibrya species-group is possibly related to the tracking of their host-plants and the complicated geological history of the island-arc system connecting Australia and East Asia.

Retroviral and pseudogene insertion sites reveal the lineage of human salivary and pancreatic amylase genes from a single gene during primate evolution

1990 ◽  
Vol 10 (6) ◽  
pp. 2513-2520
Author(s):  
L C Samuelson ◽  
K Wiebauer ◽  
C M Snow ◽  
M H Meisler
Keyword(s):  
Gene Family ◽  
Single Gene ◽  
Primate Evolution ◽  
Endogenous Retrovirus ◽  
Gene Copy ◽  
Nucleotide Sequence Analysis ◽  
Ancestral Gene ◽  
Molecular Events ◽  
Amylase Genes ◽  
History Of

We have analyzed the junction regions of inserted elements within the human amylase gene complex. This complex contains five genes which are expressed at high levels either in the pancreas or in the parotid gland. The proximal 5'-flanking regions of these genes contain two inserted elements. A gamma-actin pseudogene is located at a position 200 base pairs upstream of the first coding exon. All of the amylase genes contain this insert. The subsequent insertion of an endogenous retrovirus interrupted the gamma-actin pseudogene within its 3'-untranslated region. Nucleotide sequence analysis of the inserted elements associated with each of the five human amylase genes has revealed a series of molecular events during the recent history of this gene family. The data indicate that the entire gene family was generated during primate evolution from one ancestral gene copy and that the retroviral insertion activated a cryptic promoter.

scholarly journals Progress toward a Respiratory Syncytial Virus Vaccine

2016 ◽  
Vol 23 (3) ◽  
pp. 186-188 ◽  
Author(s):  
Kathleen M. Neuzil
Keyword(s):  
Viral Load ◽  
Respiratory Syncytial Virus ◽  
Virus Vaccine ◽  
Effective Vaccine ◽  
Vaccine Candidates ◽  
Target Populations ◽  
Link Type ◽  
History Of ◽  
Syncytial Virus ◽  
Respiratory Syncytial Virus Vaccine

ABSTRACTIn accompanying papers (P. L. Acosta, M. T. Caballero, and F. P. Polack, Clin Vaccine Immunol 23:189–195, 2016,http://dx.doi.org/10.1128/CVI.00609-15; M. Vissers, I. M. L. Ahout, M. I. de Jonge, and G. Ferwerda, Clin Vaccine Immunol 23:243–245, 2016,http://dx.doi.org/10.1128/CVI.00590-15) in this issue ofClinical and Vaccine Immunology, the history of and immune mechanisms underlying vaccine-enhanced respiratory syncytial virus (RSV) disease and of investigations of mucosal antibodies and their association with viral load in RSV-infected children, respectively, are described. This commentary discusses RSV vaccine candidates, target populations, and the challenges associated with achieving a safe and effective vaccine.

scholarly journals Associations between History of Hospitalization for Violence Victimization and Substance-Use Patterns among Adolescents: A 2017 Korean National Representative Survey

2018 ◽  
Vol 15 (7) ◽  
pp. 1543
Author(s):  
Yeji Lee ◽  
Kang-Sook Lee
Keyword(s):  
Substance Use ◽  
Drug Use ◽  
Secondary Data ◽  
Web Based ◽  
Alcohol And Drug Use ◽  
Violence Victimization ◽  
Use Patterns ◽  
Chi Squared ◽  
History Of ◽  
Victimization Experience

Violence victimization can adversely affect adolescents’ long-term health. Existing research has mainly focused on the link between victimization and substance use; however, the evidence obtained to date has been inconsistent. This study, using a Korean national representative sample, examined the association between violence victimization and substance-use patterns (including tobacco, alcohol, and drug use) in terms of sex and number of violence victimization experiences. We analyzed secondary data from the 2017 Korean Youth Risk Behavior Web-based Survey. Chi-squared test analyses and logistic regression analysis were used to examine substance use in terms of violence victimization; additionally, p-values for trends were calculated to reveal the dose-response relationship per number of violence victimization experiences. We consequently found that participants’ rates of tobacco, alcohol, and drug use were higher among those who experienced violence victimization than among those who did not. For each substance-use-related variable, the greater the violence victimization experience, the higher the odds of substance use (p for trend < 0.001). Early intervention may help prevent the development of substance use, especially among adolescents who have experienced violence victimization. Prevention efforts regarding substance abuse and violence prevention should be included in school curricula to effectively prevent adverse health consequences among adolescents.

scholarly journals A DNA investigation into the mysterious disappearance of the Rocky Mountain grasshopper, mega-pest of the 1800s

2017 ◽  
Author(s):  
W. Chapco ◽  
G. Litzenberger
Keyword(s):  
Dna Sequences ◽  
Nucleotide Diversity ◽  
Rocky Mountain ◽  
Species Group ◽  
Pest Species ◽  
History Of Agriculture ◽  
Extant Species ◽  
Remarkable Event ◽  
History Of ◽  
Major Pest

The mysterious extinction of the Rocky Mountain Grasshopper, Melanoplus spretus, a major pest species on the prairies and plains of the 1800s, is truly a remarkable event in the history of agriculture. Recently, we obtained specimens of M. spretus from museums and from 400-year-old glacial deposits in Wyoming. We report success in obtaining mitochondrial DNA sequences from both sources. This permitted us to examine two issues surrounding the species’ disappearance. First, a long-standing view that M. spretus and the extant species Melanoplus sanguinipes are (if not phase transforms of one another) sister taxa, is disputed, but cannot be rejected with certainty. Interestingly, there is some evidence that suggests there may be a closer affinity with another member of the Mexicanus species-group, Melanoplus bruneri. Second, because M. spretus still possesses considerable nucleotide diversity (1.15 ± 0.19%), a depletion of variation cannot be considered a factor contributing to its demise.

scholarly journals Gene Expression Networks in the Drosophila Genetic Reference Panel

2019 ◽  
Author(s):  
Logan J. Everett ◽  
Wen Huang ◽  
Shanshan Zhou ◽  
Mary Anna Carbone ◽  
Richard F. Lyman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transposable Elements ◽  
Dna Sequences ◽  
Quantitative Trait ◽  
Regulatory Networks ◽  
Target Genes ◽  
Reference Panel ◽  
Modern Biology ◽  
Specific Expression ◽  
Drosophila Genetic Reference Panel

SummaryA major challenge in modern biology is to understand how naturally occurring variation in DNA sequences affects complex organismal traits through networks of intermediate molecular phenotypes. Here, we performed deep RNA sequencing of 200 Drosophila Genetic Reference Panel inbred lines with complete genome sequences, and mapped expression quantitative trait loci for annotated genes, novel transcribed regions (most of which are long noncoding RNAs), transposable elements and microbial species. We identified host variants that affect expression of transposable elements, independent of their copy number, as well as microbiome composition. We constructed sex-specific expression quantitative trait locus regulatory networks. These networks are enriched for novel transcribed regions and target genes in heterochromatin and euchromatic regions of reduced recombination, and genes regulating transposable element expression. This study provides new insights regarding the role of natural genetic variation in regulating gene expression and generates testable hypotheses for future functional analyses.

scholarly journals SEMANTICS OF POEM IN «DIV TICS OF POEM IN «DIVANI LUGATI-T-TURK»

2021 ◽  
pp. 36-45
Author(s):  
Qosimjon SODIQOV ◽  
Govhar RAHMATOVA
Keyword(s):  
World Literature ◽  
Fine Art ◽  
Oral Poetry ◽  
Verbal Art ◽  
Specific Expression ◽  
Artistic Value ◽  
Aesthetic Taste ◽  
History Of ◽  
Extensive Information ◽  
The Aesthetic

Lyric songs depict how rich is the aesthetic taste of the Turkic peoples and their special love for verbal art for a long period, and the fact that they possessed artistic resources capable of competing with the most agile peoples of their time. Moreover, these songs illustrate the artistic views of the Turks. Pure lyrical experiences, with their novelty, the richness of images, and unique pathos, have always engaged the reader. The poetry of the Turkic peoples is studied as a separate phenomenon in the history of world literature. Mahmud Kashgari’s Divani lugat at-Turk provides extensive information about the foundations of Turkish poetry and its scope. We can see the first paradigms of lyric poetry in the oral poetry of the Turkic peoples in the Divani lugat at-Turk. As a great linguist of his time and an advanced thinker – Kashgari proves each word with its specific expression or a piece of poetry. Each poem in his work is unique regarding its artistic value and semantics. We can see this, especially in these lyrical poems. Even simple episodes in lyrical songs demonstrate the ability of our ancestors to express thoughts beautifully. The lyrical passages in the Divani lugat at-Turk consist of the description of the mistress, the sad moments of the separation of beloved ones, and the poems addressed to his beloved one. The issue of fine art and its location is noteworthy in them. The devices used in them play an essential role as the initial version in the context of the literature of the Turkic peoples. The author cites some examples of such poetic art: tashbih, oxymoron, metaphor, tajnis, repetition, hyperbole (mubalaga), irsali masal, etc. These devices were actively reflected in all types of poetry of the later period. This article discusses the semantics of lyrical poems in the Divani lugat at-Turk and reveals their fine art.

scholarly journals A Comparative Study of Plasma Proteins from Twenty-Nine Species of Albatrosses And Petrels (Order Procellariiformes)

2021 ◽  
Author(s):  
◽  
Peter C Harper
Keyword(s):  
Plasma Proteins ◽  
Species Group ◽  
Reference Points ◽  
Evolutionary Significance ◽  
Group Level ◽  
Family Level ◽  
Phylogenetic Conservatism ◽  
History Of ◽  
Biochemical Research

<p>The plasma proteins of 29 species of albatrosses and petrels were electrophoretically separated in acrylamide gels to clarify relationships at the species-group to family-group levels. Little in the resulting data from 472 birds seriously contests the present classification of the Procellariiformes; much of the biochemical evidence supports, confirms, and clarifies the proposals of conventional taxonomic methodology. The biochemical data give fresh insights into the interrelationships of procellariiform taxa, and highlight intriguing new problems. Sex, season, age, and other sources of non-genetic protein variation are insignificant for taxonomic purposes. Proteins of comparable value include the transferrins, some α and β globulins, albumins, prealbumins, and non-specific esterases. Genetic variations in the mobility of these proteins are useful at the genus-group level and below. Other proteins are monomorphic at genus and family level, and three are monomorphic in both number and mobility throughout the Procellariiformes; these are useful reference points for calibrating samples on different gels. One conspicuous α protein is absent in the Hydrobatidae but present in all other families; the implications of this are discussed. Polymorphic proteins at the population or species level were not detected; this conspicuous phylogenetic conservatism is discussed with regard to its possible evolutionary significance. Following a summary of the protein data; three categories of, defined probability statements, based on the biochemical and other evidence, allow speculative comment on the evolutionary relationships and history of the taxa within the Procellariiformes. The value of further biochemical research into the marine birds is emphasised.</p>

Sign in / Sign up

Export Citation Format

Share Document