Colour plasticity in response to social context and parasitic infection in a self-fertilizing fish

Many animal species rely on changes in body coloration to signal social dominance, mating readiness and health status to conspecifics, which can in turn influence reproductive success, social dynamics and pathogen avoidance in natural populations. Such colour changes are thought to be controlled by genetic and environmental conditions, but their relative importance is difficult to measure in natural populations, where individual genetic variability complicates data interpretation. Here, we studied shifts in melanin-related body coloration in response to social context and parasitic infection in two naturally inbred lines of a self-fertilizing fish to disentangle the relative roles of genetic background and individual variation. We found that social context and parasitic infection had a significant effect on body coloration that varied between genetic lines, suggesting the existence of genotype by environment interactions. In addition, individual variation was also important for some of the colour attributes. We suggest that the genetic background drives colour plasticity and that this can maintain phenotypic variation in inbred lines, an adaptive mechanism that may be particularly important when genetic diversity is low.

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The transposable elements of the Drosophila serrata reference panel

10.1101/2020.06.11.146431 ◽

2020 ◽

Author(s):

Zachary Tiedeman ◽

Sarah Signor

Keyword(s):

Transposable Elements ◽

Transposable Element ◽

Copy Number ◽

Genetic Background ◽

Natural Populations ◽

Inbred Lines ◽

Transposable Element Insertion ◽

Defense Systems ◽

Drosophila Serrata ◽

Transposable Element Copy

AbstractTransposable elements are an important element of the complex genomic ecosystem, proving to be both adaptive and deleterious - repressed by the piRNA system and fixed by selection. Transposable element insertion also appears to be bursty – either due to invasion of new transposable elements that are not yet repressed, de-repression due to instability of organismal defense systems, stress, or genetic variation in hosts. Here, we characterize the transposable element landscape in an important model Drosophila, D. serrata, and investigate variation in transposable element copy number between genotypes and in the population at large. We find that a subset of transposable elements are clearly related to elements annotated in D. melanogaster and D. simulans, suggesting they spread between species more recently than other transposable elements. We also find that transposable elements do proliferate in particular genotypes, and that often if an individual is host to a proliferating transposable element, it is host to more than one proliferating transposable element. In addition, if a transposable element is active in a genotype, it is often active in more than one genotype. This suggests that there is an interaction between the host and the transposable element, such as a permissive genetic background and the presence of potentially active transposable element copies. In natural populations an active transposable element and a permissive background would not be held in association as in inbred lines, suggesting the magnitude of the burst would be much lower. Yet many of the inbred lines have actively proliferating transposable elements suggesting this is an important mechanism by which transposable elements maintain themselves in populations.

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Studies of esterase 6 in Drosophila melanogaster: XIV. Variation of esterase 6 levels controlled by unlinked genes in natural populations

Genetics Research ◽

10.1017/s0016672300025891 ◽

1984 ◽

Vol 43 (2) ◽

pp. 181-190 ◽

Cited By ~ 7

Author(s):

Craig S. Tepper ◽

Anne L. Terry ◽

James E. Holmes ◽

Rollin C. Richmond

Keyword(s):

Drosophila Melanogaster ◽

Structural Gene ◽

X Chromosome ◽

Genetic Background ◽

Natural Populations ◽

Regulatory Elements ◽

Regulatory Locus ◽

The Third ◽

Esterase 6 ◽

Activity Modifiers

SUMMARYThe esterase 6 (Est-6) locus in Drosophila melanogaster is located on the third chromosome and is the structural gene for a carboxylesterase (E.C.3.1.1.1) and is polymorphic for two major electromorphs (slow and fast). Isogenic lines containing X chromosomes extracted from natural populations and substituted into a common genetic background were used to detect unlinked factors that affect the activity of the Est-6 locus. Twofold activity differences of esterase 6 (EST 6) were found among males from these derived lines, which differ only in their X chromosome. These unlinked activity modifiers identify possible regulatory elements. Immunoelectrophoresis was used to estimate quantitatively the levels of specific cross-reacting material in the derived lines. The results show that the variation in activity is due to differences in the amount of EST 6 present. The data are consistent with the hypothesis that there is at least one locus on the X chromosome that regulates the synthesis of EST 6 and that this regulatory locus may be polymorphic in natural populations.

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The impact of genetic background and cell lineage on the level and pattern of gene expression in position effect variegation

Epigenetics & Chromatin ◽

10.1186/s13072-019-0314-5 ◽

2019 ◽

Vol 12 (1) ◽

Author(s):

Sidney H. Wang ◽

Sarah C. R. Elgin

Keyword(s):

Genetic Variants ◽

Genetic Background ◽

Position Effect ◽

Cell Lineage ◽

Inbred Lines ◽

Position Effect Variegation ◽

Fourth Chromosome ◽

Heterochromatin Formation ◽

Effect Variegation ◽

The Impact

Abstract Background Chromatin-based transcriptional silencing is often described as a stochastic process, largely because of the mosaic expression observed in position effect variegation (PEV), where a euchromatic reporter gene is silenced in some cells as a consequence of juxtaposition with heterochromatin. High levels of variation in PEV phenotypes are commonly observed in reporter stocks. To ascertain whether background mutations are the major contributors to this variation, we asked how much of the variation is determined by genetic variants segregating in the population, examining both the level and pattern of expression using the fruit fly, Drosophila melanogaster, as the model. Results Using selective breeding of a fourth chromosome PEV reporter line, 39C-12, we isolated two inbred lines exhibiting contrasting degrees of variegation (A1: low expression, D1: high expression). Within each inbred population, remarkable similarity is observed in the degree of variegation: 90% of the variation between the two inbred lines in the degree of silencing can be explained by genotype. Further analyses suggest that this result reflects the combined effect of multiple independent trans-acting loci. While the initial observations are based on a PEV phenotype scored in the fly eye (hsp70-white reporter), similar degrees of silencing were observed using a beta-gal reporter scored across the whole fly. Further, the pattern of variegation becomes almost identical within each inbred line; significant pigment enrichment in the same quadrant of the eye was found for both A1 and D1 lines despite different degrees of expression. Conclusions The results indicate that background genetic variants play the major role in determining the variable degrees of PEV commonly observed in laboratory stocks. Interestingly, not only does the degree of variegation become consistent in inbred lines, the patterns of variegation also appear similar. Combining these observations with the spreading model for local heterochromatin formation, we propose an augmented stochastic model to describe PEV in which the genetic background drives the overall level of silencing, working with the cell lineage-specific regulatory environment to determine the on/off probability at the reporter locus in each cell. This model acknowledges cell type-specific events in the context of broader genetic impacts on heterochromatin formation.

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Complex relationships between physiological stress and endoparasite infections in natural populations

Current Zoology ◽

10.1093/cz/zoaa029 ◽

2020 ◽

Vol 66 (5) ◽

pp. 449-457 ◽

Cited By ~ 1

Author(s):

Claudia Romeo ◽

Lucas A Wauters ◽

Francesca Santicchia ◽

Ben Dantzer ◽

Rupert Palme ◽

...

Keyword(s):

Physiological Stress ◽

Parasitic Infection ◽

Natural Populations ◽

Nematode Species ◽

Gastrointestinal Parasites ◽

Sciurus Carolinensis ◽

Mediated Effects ◽

Fecal Glucocorticoid Metabolites ◽

Immune Mediated ◽

Complex Relationships

Abstract Short-term elevation of glucocorticoids (GCs) is one of the major physiological mechanisms by which vertebrates cope with challenging environmental or social factors (stressors). However, when exposure to stressors occurs repeatedly or over a prolonged period of time, animals may experience chronic elevation of GCs, which reduces the immune response efficiency and can lead to higher intensity of parasitic infection. Here, we used invasive gray squirrels Sciurus carolinensis introduced in Northern Italy and their 2 most prevalent gastrointestinal parasites, the nematode Strongyloides robustus and coccidia of the genus Eimeria, as a model to investigate relationships among macroparasite infection and concentrations of fecal glucocorticoid metabolites (FGMs), an integrated measure of circulating GCs. Our results revealed an association of FGMs with infection by St. robustus, but not with coccidia. Individuals with higher FGMs appear to be responsible for the greatest St. robustus egg shedding within gray squirrel populations, thus possibly acting as superspreaders. However, FGMs were negatively associated with adult St. robustus, suggesting that the abundance of adults of this nematode species does not induce elevation in FGMs, but is only affected by it through immune-mediated effects on its fecundity. Finally, the relationship between St. robustus (both eggs and adult parasites) and FGMs was not linear, suggesting that only high levels of physiological stress influence parasite infection. Our findings highlight that the direction and magnitude of the stress–infection relationship may depend not only on the specific host–parasite system, but also on the different life stages of the same parasite.

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FYI: TMI: Toward a holistic social theory of information overload

First Monday ◽

10.5210/fm.v16i3.3051 ◽

2011 ◽

Cited By ~ 1

Author(s):

Anthony Lincoln

Keyword(s):

Social Context ◽

Social Theory ◽

Social Dynamics ◽

Information Overload ◽

Social Issues ◽

Rational Behavior ◽

Information Usage ◽

The Social ◽

Critical Understanding ◽

Theory Of Information

Research into information overload has been extensive and cross-disciplinary, producing a multitude of suggested causes and posed solutions. I argue that many of the conclusions arrived at by existing research, while laudable in their inventiveness and/or practicality, miss the mark by viewing information overload as a problem that can be understood (or even solved) by purely rational means. Such a perspective lacks a critical understanding in human information usage: much in the same way that economic models dependent on rationality for their explanations or projections fail (often spectacularly, as recent history attests), models that rely too heavily upon the same rational behavior, and not heavily enough upon the interplay of actual social dynamics—power, reputation, norms, and others—in their attempts to explain, project, or address information overload prove bankrupt as well. Furthermore, even research that displays greater awareness of the social context in which overload exists often reveals a similar rationality in its conceptualization. That is, often the same “social” approaches that offer potential advantages (in mitigating information overload) over their “non-social” counterparts paradoxically raise new problems, requiring a reappraisal of overload that takes social issues into account holistically.

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Rapid body color brightening is associated with exposure to a stressor in an Anolis lizard

Canadian Journal of Zoology ◽

10.1139/cjz-2016-0200 ◽

2017 ◽

Vol 95 (3) ◽

pp. 213-219 ◽

Cited By ~ 3

Author(s):

Jane F.F. Boyer ◽

Lindsey Swierk

Keyword(s):

Color Change ◽

Light Exposure ◽

Natural Populations ◽

Body Color ◽

Anolis Lizard ◽

Body Coloration ◽

Body Regions ◽

Before And After ◽

Three Body ◽

Typical Skin

Many species use color change to optimize body coloration to changing environmental conditions, and drivers of rapid color change in natural populations are numerous and poorly understood. We examined factors influencing body coloration in the Water Anole (Anolis aquaticus Taylor, 1956), a lizard possessing color-changing stripes along the length of its body. We quantified the color of three body regions (the eye stripe, lateral stripe, and dorsum) before and after exposure to a mild stressor (handling and restraint). Based on current understanding of the genus Anolis Daudin, 1802, we hypothesized that exposure to a stressor would generate genus-typical skin darkening (i.e., increased melanism). Contrary to expectations, stress consistently brightened body coloration: eye and lateral stripes transitioned from brown to pale blue and green and the dorsum became lighter brown. Sex, size, and body temperature did not correlate with any aspect of body coloration, and a laboratory experiment confirmed that light exposure did not drive brightening. We propose that color change may serve to reduce conspicuousness through disruptive camouflage; lizards tended to display brighter stripes on mottled green–brown substrates. Together, these results improve our understanding of Anolis color change diversity and emphasize the need for a broader interpretation of the mechanism and functions of color change across taxa.

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The Evolution of Fluoroquinolone-Resistance inMycobacterium tuberculosisis Modulated by the Genetic Background

10.1101/659045 ◽

2019 ◽

Author(s):

Rhastin A. D. Castro ◽

Amanda Ross ◽

Lujeko Kamwela ◽

Miriam Reinhard ◽

Chloé Loiseau ◽

...

Keyword(s):

Genetic Variation ◽

Genetic Background ◽

Natural Populations ◽

Genomic Analysis ◽

Experimental Treatment ◽

Clinical Isolates ◽

Fluoroquinolone Resistance ◽

Treatment Regimens ◽

Resistance Evolution

AbstractFluoroquinolones (FQ) form the backbone in experimental treatment regimens against drug-susceptible tuberculosis. However, little is known on whether the genetic variation present in natural populations ofMycobacterium tuberculosis(Mtb) affects the evolution of FQ-resistance (FQ-R). To investigate this question, we used a set ofMtbstrains that included nine genetically distinct drug-susceptible clinical isolates, and measured their frequency of resistance to the FQ ofloxacin (OFX)in vitro. We found that theMtbgenetic background led to differences in the frequency of OFX-resistance (OFX-R) that spanned two orders of magnitude and substantially modulated the observed mutational profiles for OFX-R. Furtherin vitroassays showed that the genetic background also influenced the minimum inhibitory concentration and the fitness effect conferred by a given OFX-R mutation. To test the clinical relevance of ourin vitrowork, we surveyed the mutational profile for FQ-R in publicly available genomic sequences from clinicalMtbisolates, and found substantialMtblineage-dependent variability. Comparison of the clinical and thein vitromutational profiles for FQ-R showed that 45% and 19% of the variability in the clinical frequency of FQ-RgyrAmutations in Lineage 2 and Lineage 4 strains, respectively, can be attributed to howMtbevolves FQ-Rin vitro. As theMtbgenetic background strongly influenced the evolution of FQ-Rin vitro, we conclude that the genetic background ofMtbalso impacts the evolution of FQ-R in the clinic.SignificanceNewer generations of fluoroquinolones form the backbone in many experimental treatment regimens againstM. tuberculosis(Mtb). While the genetic variation in natural populations ofMtbcan influence resistance evolution to multiple different antibiotics, it is unclear whether it modulates fluoroquinolone-resistance evolution as well. Using a combination ofin vitroassays coupled with genomic analysis of clinical isolates, we provide the first evidence illustrating theMtbgenetic background’s substantial role in fluoroquinolone-resistance evolution, and highlight the importance of bacterial genetics when studying the prevalence of fluoroquinolone-resistance inMtb. Our work may provide insights into how to maximize the timespan in which fluoroquinolones remain effective in clinical settings, whether as part of current standardized regimens, or in new regimens againstMtb.

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Privatisation rescues function following loss of cooperation

eLife ◽

10.7554/elife.38594 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 9

Author(s):

Sandra Breum Andersen ◽

Melanie Ghoul ◽

Rasmus L Marvig ◽

Zhuo-Bin Lee ◽

Søren Molin ◽

...

Keyword(s):

Cystic Fibrosis ◽

Social Dynamics ◽

Iron Acquisition ◽

Natural Populations ◽

Lung Infection ◽

Theoretical Studies ◽

Whole Genome ◽

Iron Availability ◽

The Social ◽

Potential Impact

A single cheating mutant can lead to the invasion and eventual eradication of cooperation from a population. Consequently, cheat invasion is often considered equal to extinction in empirical and theoretical studies of cooperator-cheat dynamics. But does cheat invasion necessarily equate extinction in nature? By following the social dynamics of iron metabolism in Pseudomonas aeruginosa during cystic fibrosis lung infection, we observed that individuals evolved to replace cooperation with a ‘private’ behaviour. Phenotypic assays showed that cooperative iron acquisition frequently was upregulated early in infection, which, however, increased the risk of cheat invasion. With whole-genome sequencing we showed that if, and only if, cooperative iron acquisition is lost from the population, a private system was upregulated. The benefit of upregulation depended on iron availability. These findings highlight the importance of social dynamics of natural populations and emphasizes the potential impact of past social interaction on the evolution of private traits.

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Dissecting genetic and sex-specific sources of host heterogeneity in pathogen shedding and spread

PLoS Pathogens ◽

10.1371/journal.ppat.1009196 ◽

2021 ◽

Vol 17 (1) ◽

pp. e1009196

Author(s):

Jonathon A. Siva-Jothy ◽

Pedro F. Vale

Keyword(s):

Viral Load ◽

Individual Variation ◽

Disease Transmission ◽

Genetic Background ◽

Pathogen Transmission ◽

Published Data ◽

Virus Shedding ◽

Transmission Potential ◽

Sources Of Variation ◽

Host Heterogeneity

Host heterogeneity in disease transmission is widespread but precisely how different host traits drive this heterogeneity remains poorly understood. Part of the difficulty in linking individual variation to population-scale outcomes is that individual hosts can differ on multiple behavioral, physiological and immunological axes, which will together impact their transmission potential. Moreover, we lack well-characterized, empirical systems that enable the quantification of individual variation in key host traits, while also characterizing genetic or sex-based sources of such variation. Here we used Drosophila melanogaster and Drosophila C Virus as a host-pathogen model system to dissect the genetic and sex-specific sources of variation in multiple host traits that are central to pathogen transmission. Our findings show complex interactions between genetic background, sex, and female mating status accounting for a substantial proportion of variance in lifespan following infection, viral load, virus shedding, and viral load at death. Two notable findings include the interaction between genetic background and sex accounting for nearly 20% of the variance in viral load, and genetic background alone accounting for ~10% of the variance in viral shedding and in lifespan following infection. To understand how variation in these traits could generate heterogeneity in individual pathogen transmission potential, we combined measures of lifespan following infection, virus shedding, and previously published data on fly social aggregation. We found that the interaction between genetic background and sex explained ~12% of the variance in individual transmission potential. Our results highlight the importance of characterising the sources of variation in multiple host traits to understand the drivers of heterogeneity in disease transmission.

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Population-level survey of loss-of-function mutations revealed that background dependent fitness genes are rare and functionally related in yeast

10.1101/2021.08.25.457624 ◽

2021 ◽

Author(s):

Elodie Caudal ◽

Anne Friedrich ◽

Marion Garin ◽

Jing Hou ◽

Joseph Schacherer

Keyword(s):

Genetic Background ◽

Genetic Interaction ◽

Natural Populations ◽

Interaction Network ◽

Population Level ◽

Continuous Variation ◽

Loss Of Function ◽

Individual Level ◽

Cytoplasmic Transport ◽

Natural Isolates

AbstractIn natural populations, the same mutation can lead to different phenotypic outcomes due to the genetic variation that exists among individuals. Such genetic background effects are commonly observed, including in the context of many human diseases. However, systematic characterization of these effects at the species level is still lacking to date. Here, we sought to comprehensively survey background-dependent traits associated with gene loss-of-function (LoF) mutations in 39 natural isolates of Saccharomyces cerevisiae using a transposon saturation strategy. By analyzing the modeled fitness variability of a total of 4,469 genes, we found that 15% of them, when impacted by a LoF mutation, exhibited a significant gain- or loss-of-fitness phenotype in certain natural isolates compared to the reference strain S288C. Out of these 632 genetic background-dependent fitness genes identified, a total of 2/3 show a continuous variation across the population while 1/3 are specific to a single genetic background. Genes related to mitochondrial function are significantly overrepresented in the set of genes showing a continuous variation and display a potential functional rewiring with other genes involved in transcription and chromatin remodeling as well as in nuclear-cytoplasmic transport. Such rewiring effects are likely modulated by both the genetic background and the environment. While background-specific cases are rare and span diverse cellular processes, they can be functionally related at the individual level. All background-dependent fitness genes tend to have an intermediate connectivity in the global genetic interaction network and have shown relaxed selection pressure at the population level, highlighting their potential evolutionary characteristics.

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