A Loss or a Gain, Is It Not All the Same?
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ABSTRACT:
SUBMITTER: Poot M
PROVIDER: S-EPMC4862398 | biostudies-literature | 2016 Apr
REPOSITORIES: biostudies-literature
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Project description:The outcome of competition between different reproductive strategies within a single species can be used to infer selective advantage of the winning strategy. Where multiple populations have independently lost or gained sexual reproduction it is possible to investigate whether the advantage is contingent on local conditions. In the New Zealand stick insect Clitarchus hookeri, three populations are distinguished by recent change in reproductive strategy and we determine their likely origins. One parthenogenetic population has established in the United Kingdom and we provide evidence that sexual reproduction has been lost in this population. We identify the sexual population from which the parthenogenetic population was derived, but show that the UK females have a post-mating barrier to fertilisation. We also demonstrate that two sexual populations have recently arisen in New Zealand within the natural range of the mtDNA lineage that otherwise characterizes parthenogenesis in this species. We infer independent origins of males at these two locations using microsatellite genotypes. In one population, a mixture of local and nonlocal alleles suggested males were the result of invasion. Males in another population were most probably the result of loss of an X chromosome that produced a male phenotype in situ. Two successful switches in reproductive strategy suggest local competitive advantage for outcrossing over parthenogenetic reproduction. Clitarchus hookeri provides remarkable evidence of repeated and rapid changes in reproductive strategy, with competitive outcomes dependent on local conditions.
| S-EPMC6852293 | biostudies-literature
Project description: Not available
| S-EPMC5056811 | biostudies-literature
Project description:We compared intron positions in conserved regions of 3479 orthologous gene pairs from Plasmodium falciparum and Plasmodium yoelii, which likely diverged >or=100 million years ago (Mya). Only 27 out of 2212 positions were specific to one of the two species. Intron presence in related species shows that at least 19 and possibly 26 of the changes are due to intron loss, depending on phylogeny. The implied intron loss and gain rates are much lower than previously estimated for nematodes, arthropods, fungi, and plants, and are comparable only with the rates in vertebrates. That all observed changes were exact, occurring without loss or gain of flanking coding sequence, suggests intron loss via an mRNA intermediate, as does a nonsignificant trend toward loss of introns at adjacent positions. Many of the intron changes occurred in genes encoding proteins involved in nucleic acid-related processes, as previously found for intron gains in nematodes. Two changes occurred in the chloroquine resistance transporter, suggesting a role for positive selection in intron loss in Plasmodium. The dearth of intron loss and gain could be explained by the lack of known transposable elements in Plasmodium, since transposable elements and/or reverse transcriptase are thought to be necessary for both processes. The observed pattern suggests that the availability of stochastic intron loss and gain mutations can be a major determinant of changes in intron number.
| S-EPMC1473185 | biostudies-literature
Project description: Not available
| S-EPMC10874118 | biostudies-literature
Project description:Comparison between transcriptomes of dash mutants vs WT plants and ectopic expression of 35S::DASH in hairy roots versus empty vector Loss of function: 3 WT plants A17 at 8 days after pollination and 3 dash mutant plants at 8 days afer pollination. Gain of function transformants: 3 transformed plants containing empty vector and 4 transformed plants containing 35S::DASH Total RNA was extracted using a modified cetyltrimethylammonium bromide method (Verdier et al., 2008). 5ug of total RNA from each sample was purified (RNeasy MinElute Cleanup kit; Qiagen) according to the manufacturer?s instructions. RNA was quantified and evaluated for purity using an ND-1000 Nanodrop Spectrophotometer (NanoDrop Technologies) and a Bioanalyzer 2100 (Agilent). The Affymetrix M. truncatula GeneChip Array (Affymetrix) was used for expression analysis during seed development. RNA from three (for dash mutant analysis) and four (for DASH ectopic expression analysis) independent biological replicates were analysed for each time point. Probe synthesis/labelling was carried out from 500 ng of RNA using the GeneChip 3?IVT express kit, according to the manufacturer?s instructions (Affymetrix). Array hybridization, scanning, and data normalization were performed as described by Benedito et al., (2008). Each file from the hybridized Affymetrix array was exported from GeneChip Operating Software version 1.4 (Affymetrix) and imported into Robust Multiarray Average Express (Irizarry et al., 2003) for global normalization. Presence/absence call for each probe set to remove background noise was obtained using dCHIP (Li and Wong, 2001). To identify probe sets differentially expressed in dash mutant vs WT control, the R package Anapuce (J. Aubert, UMR 518 AgroParisTech/INRA) was used. For each probe set, a paired t-test was performed on the log2 expression data from three arrays (3 independent biological repeats for 8 dap data), assuming that the variance of the log expression was the same for all transcripts per genotype. Spots with extreme specific variance, too low or too high, were excluded from the statistical analysis (details on the procedure given in Gagnot et al., 2008). P-values were adjusted by the Benjamini-Hochberg method (Benjamini and Hochberg, 1995), which controls the family-wise error rate.
2015-01-20 | E-GEOD-58117 | biostudies-arrayexpress
Project description:BACKGROUND: It is widely accepted that orthologous genes have lost or gained introns throughout evolution. However, the specific mechanisms that generate these changes have proved elusive. Introns are known to affect nearly every level of gene expression. Therefore, understanding their mechanism of evolution after their initial fixation in eukaryotes is pertinent to understanding the means by which organisms develop greater regulation and complexity. RESULTS: To investigate possible mechanisms of intron gain and loss, we identified 189 intron gain and 297 intron loss events among 11 Drosophila species. We then investigated these events for signatures of previously proposed mechanisms of intron gain and loss. This work constitutes the first comprehensive study into the specific mechanisms that may generate intron gains and losses in Drosophila. We report evidence of intron gain via transposon insertion; the first intron loss that may have occurred via non-homologous end joining; intron gains via the repair of a double strand break; evidence of intron sliding; and evidence that internal or 5' introns may not frequently be deleted via the self-priming of reverse transcription during mRNA-mediated intron loss. Our data also suggest that the transcription process may promote or result in intron gain. CONCLUSION: Our findings support the occurrence of intron gain via transposon insertion, repair of double strand breaks, as well as intron loss via non-homologous end joining. Furthermore, our data suggest that intron gain may be enabled by or due to transcription, and we shed further light on the exact mechanism of mRNA-mediated intron loss.
| S-EPMC3296678 | biostudies-literature
Project description:Little is known about the patterns of intron gain and loss or the relative contributions of these two processes to gene evolution. To investigate the dynamics of intron evolution, we analyzed orthologous genes from four filamentous fungal genomes and determined the pattern of intron conservation. We developed a probabilistic model to estimate the most likely rates of intron gain and loss giving rise to these observed conservation patterns. Our data reveal the surprising importance of intron gain. Between about 150 and 250 gains and between 150 and 350 losses were inferred in each lineage. We discuss one gene in particular (encoding 1-phosphoribosyl-5-pyrophosphate synthetase) that displays an unusually high rate of intron gain in multiple lineages. It has been recognized that introns are biased towards the 5' ends of genes in intron-poor genomes but are evenly distributed in intron-rich genomes. Current models attribute this bias to 3' intron loss through a poly-adenosine-primed reverse transcription mechanism. Contrary to standard models, we find no increased frequency of intron loss toward the 3' ends of genes. Thus, recent intron dynamics do not support a model whereby 5' intron positional bias is generated solely by 3'-biased intron loss.
| S-EPMC532390 | biostudies-literature
Project description:BackgroundGenome comparisons across deep phylogenetic divergences have revealed that spliceosomal intron gain and loss are common evolutionary events. However, because of the deep divergences involved in these comparisons, little is understood about how these changes occur, particularly in the case of intron gain. To ascertain mechanisms of intron gain and loss, we compared five relatively closely related genomes from the yeast Cryptococcus.ResultsWe observe a predominance of intron loss over gain and identify a relatively slow intron loss rate in Cryptococcus. Some genes preferentially lose introns and a large proportion of intron losses occur in the middle of genes (so called internal intron loss). Finally, we identify a gene that displays a differential number of introns in a repetitive DNA region.ConclusionBased the observed patterns of intron loss and gain, population resequencing and population genetic analysis, it appears that recombination causes the widely observed but poorly understood phenomenon of internal intron loss and that DNA repeat expansion can create new introns in a population.
| S-EPMC2395259 | biostudies-literature
Project description:Human decision-making behaviors in social contexts are largely driven by fairness considerations. The dual-process model suggests that in addition to cognitive processes, emotion contributes to economic decision-making. Although humor, as an effective emotional regulation strategy to induce positive emotion, may influence an individual's emotional state and decision-making behavior, previous studies have not examined how humor modulates fairness-related responses in the gain and loss contexts simultaneously. This study uses the Ultimatum Game (UG) in gain and loss contexts to explore this issue. The results show, in the gain context, viewing humorous pictures compared to humorless pictures increased acceptance rates and this effect was moderated by the offer size. However, we did not find the same effect in the loss context. These findings indicate that humor's affection for fairness considerations may depend on the context and provide insight into the finite power of humor in human sociality, cooperation and norm compliance.
| S-EPMC6330900 | biostudies-other
Project description:We explored the relationship between neighborhood socioeconomic disadvantage (NSED) and gestational weight gain and loss and if the association differed by race. A census tract level NSED index (categorized as low, mid-low, mid-high, and high) was generated from 12 measures from the 2000 US Census data. Gestational weight gain and other individual-level characteristics were derived from vital birth records for Allegheny County, PA for 2003-2010 (n = 55,608). Crude and adjusted relative risks were estimated using modified multilevel Poisson regression models to estimate the association between NSED and excessive and inadequate gestational weight gain (GWG) and weight loss (versus adequate GWG). Black women lived in neighborhoods that were more likely to be socioeconomically disadvantaged compared to white women. Almost 55% of women gained an excessive amount of weight during pregnancy, and 2% lost weight during pregnancy. Black women were more likely than white women to have inadequate weight gain or weight loss. Mid-high (aRR = 1.3, 95% CI 1.2, 1.3) and high (aRR = 1.5, 95% CI 1.5, 1.6) NSED compared to low NSED was associated with inadequate weight gain while NSED was not associated with excessive weight gain. Among black women, high versus low NSED was associated with weight loss during pregnancy (RR = 1.6, 95% CI 1.1, 2.5). Among white women, each level of NSED compared to low NSED was associated with weight loss during pregnancy. This study demonstrates how neighborhood socioeconomic characteristics can contribute to our understanding of inadequate weight gain and weight loss during pregnancy, having implications for future research and interventions designed to advance pregnancy outcomes.
| S-EPMC3954468 | biostudies-literature