Detection vs selection: integration of genetic, epigenetic and environmental cues in fluctuating environments

ArticleThere are many inputs during development that influence an organism's fit to current or upcoming environments. These include genetic effects, transgenerational epigenetic influences, environmental cues and developmental noise, which are rarely investigated in the same formal framework. We study an analytically tractable evolutionary model, in which cues are integrated to determine mature phenotypes in fluctuating environments. Environmental cues received during development and by the mother as an adult act as detection-based (individually observed) cues. The mother's phenotype and a quantitative genetic effect act as selection-based cues (they correlate with environmental states after selection). We specify when such cues are complementary and tend to be used together, and when using the most informative cue will predominate. Thus, we extend recent analyses of the evolutionary implications of subsets of these effects by providing a general diagnosis of the conditions under which detection and selection-based influences on development are likely to evolve and coexist.This work was supported by a Leverhulme Trust International Network Grant to the four authors and by a grant from the Swedish Research Council (621-2010-5437) to O.L

Ecological genetic conflict: Genetic architecture can shift the balance between local adaptation and plasticity

This is the author accepted manuscript. The final version is available from University of Chicago Press via the DOI in this record.Genetic polymorphism can contribute to local adaptation in heterogeneous habitats, for instance as a single locus with alleles adapted to different habitats. Phenotypic plasticity can also contribute to trait variation across habitats, through developmental responses to habitat-specific cues. We show that the genetic architecture of genetically polymorphic and plasticity loci may influence the balance between local adaptation and phenotypic plasticity. These effects of genetic architecture are instances of ecological genetic conflict. A reduced effective migration rate for genes tightly linked to a genetic polymorphism provides an explanation for the effects, and they can occur both for a single trait and for a syndrome of co-adapted traits. Using individualbased simulations and numerical analysis, we investigate how among-habitat genetic polymorphism and phenotypic plasticity depend on genetic architecture. We also study the evolution of genetic architecture itself, in the form of rates of recombination between genetically polymorphic loci and plasticity loci. Our main result is that for plasticity genes that are unlinked to loci with between-habitat genetic polymorphism, the slope of a reaction norm is steeper in comparison with the slope favored by plasticity genes that are tightly linked to genes for local adaptation.This work was supported by grants from the Carl Trygger Foundation (CTS 15292) to OL and by a Leverhulme Trust International Network Grant to SRXD, PH, OL, and JMM

Minder mineralenverlies in de substraatteelt : een economische analyse van opties

De overheid wil stapsgewijs de lozingen van mineralen door glastuinbouwbedrijven met substraatteelt naar de omgeving terugdringen. In 2027 moeten deze lozingen vrijwel nul zijn. Onderzocht is welke maatregelen daartoe door de bedrijven genomen kunnen worden en welke kosten die met zich mee zullen brengen. The Dutch government wants to reduce the release (leaching) of nutrients from greenhouse horticultural firms with substrate-grown crops into the environment. These releases must be practically nil in 2027. This study examined which measures could be taken by the firms to comply with this objective and the associated costs

The evolution of social learning as phenotypic cue integration

This is the author accepted manuscript. The final version is available from the Royal Society via the DOI in this recordMost analyses of the origins of cultural evolution focus on when and where social learning prevails over individual learning, overlooking the fact that there are other developmental inputs that influence phenotypic fit to the selective environment. This raises the question how the presence of other cue ‘channels’ affects the scope for social learning. Here, we present a model that considers the simultaneous evolution of (i) multiple forms of social learning (involving vertical or horizontal learning based on either prestige or conformity biases) within the broader context of other evolving inputs on phenotype determination, including (ii) heritable epigenetic factors, (iii) individual learning, (iv) environmental and cascading maternal effects, (v) conservative bet-hedging and (vi) genetic cues.In fluctuating environments that are autocorrelated (and hence predictable), we find that social learning from members of the same generation (horizontal social learning) explains the large majority of phenotypic variation, whereas other cues are much less important. Moreover, social learning based on prestige biases typically prevails in positively autocorrelated environments, whereas conformity biases prevail in negatively autocorrelated environments. Only when environments are unpredictable or horizontal social learning is characterised by an intrinsically low information content, other cues such as conservative bet-hedging or vertical prestige biases prevail.Leverhulme TrustSwedish Research Counci

Detailed Analysis of Scatter Contribution from Different Simulated Geometries of X-ray Detectors.

Scattering is one of the main issues left in planar mammography examinations, as it degrades the quality of the image and complicates the diagnostic process. Although widely used, anti-scatter grids have been found to be inefficient, increasing the dose delivered, the equipment price and not eliminating all the scattered radiation. Alternative scattering reduction methods, based on postprocessing algorithms using Monte Carlo (MC) simulations, are being developed to substitute anti-scatter grids. Idealized detectors are commonly used in the simulations for the purpose of simplification. In this study, the scatter distribution of three detector geometries is analyzed and compared: Case 1 makes use of idealized detector geometry, Case 2 uses a scintillator plate and Case 3 uses a more realistic detector simulation, based on the structure of an indirect mammography X-ray detector. This paper demonstrates that common configuration simplifications may introduce up to 14% of underestimation of the scatter in simulation results

Activation of CD44/PAK1/AKT signaling promotes resistance to FGFR1 inhibition in squamous-cell lung cancer

Lung cancer is the leading cause of cancer-related deaths worldwide. Fibroblast growth factor receptor 1 (FGFR1) gene amplification is one of the most prominent and potentially targetable genetic alterations in squamous-cell lung cancer (SQCLC). Highly selective tyrosine kinase inhibitors have been developed to target FGFR1; however, resistance mechanisms originally existing in patients or acquired during treatment have so far led to limited treatment efficiency in clinical trials. In this study we performed a wide-scale phosphoproteomic mass-spectrometry analysis to explore signaling pathways that lead to resistance toward FGFR1 inhibition in lung cancer cells that display (i) intrinsic, (ii) pharmacologically induced and (iii) mutationally induced resistance. Additionally, we correlated AKT activation to CD44 expression in 175 lung cancer patient samples. We identified a CD44/PAK1/AKT signaling axis as a commonly occurring resistance mechanism to FGFR1 inhibition in lung cancer. Co-inhibition of AKT/FGFR1, CD44/FGFR1 or PAK1/FGFR1 sensitized ‘intrinsically resistant’ and ‘induced-resistant’ lung-cancer cells synergetically to FGFR1 inhibition. Furthermore, strong CD44 expression was significantly correlated with AKT activation in SQCLC patients. Collectively, our phosphoproteomic analysis of lung-cancer cells resistant to FGFR1 inhibitor provides a large data library of resistance-associated phosphorylation patterns and leads to the proposal of a common resistance pathway comprising CD44, PAK1 and AKT activation. Examination of CD44/PAK1/AKT activation could help to predict response to FGFR1 inhibition. Moreover, combination between AKT and FGFR1 inhibitors may pave the way for an effective therapy of patients with treatment-resistant FGFR1-dependent lung cancer

Still a Host of Hosts for Wolbachia: Analysis of Recent Data Suggests That 40% of Terrestrial Arthropod Species Are Infected

Wolbachia are intracellular bacteria that manipulate the reproduction of their arthropod hosts in remarkable ways. They are predominantly transmitted vertically from mother to offspring but also occasionally horizontally between species. In doing so, they infect a huge range of arthropod species worldwide. Recently, a statistical analysis estimated the infection frequency of Wolbachia among arthropod hosts to be 66%. At the same time, the authors of this analysis highlighted some weaknesses of the underlying data and concluded that in order to improve the estimate, a larger number of individuals per species should be assayed and species be chosen more randomly. Here we apply the statistical approach to a more appropriate data set from a recent survey that tested both a broad range of species and a sufficient number of individuals per species. Indeed, we find a substantially different infection frequency: We now estimate the proportion of Wolbachia-infected species to be around 40% which is lower than the previous estimate but still points to a surprisingly high number of arthropods harboring the bacteria. Notwithstanding this difference, we confirm the previous result that, within a given species, typically most or only a few individuals are infected. Moreover, we extend our analysis to include several reproductive parasites other than Wolbachia that were also screened for in the aforementioned empirical survey. For these symbionts we find a large variation in estimated infection frequencies and corroborate the finding that Wolbachia are the most abundant endosymbionts among arthropod species

A New Model and Method for Understanding Wolbachia-Induced Cytoplasmic Incompatibility

Wolbachia are intracellular bacteria transmitted almost exclusively vertically through eggs. In response to this mode of transmission, Wolbachia strategically manipulate their insect hosts' reproduction. In the most common manipulation type, cytoplasmic incompatibility, infected males can only mate with infected females, but infected females can mate with all males. The mechanism of cytoplasmic incompatibility is unknown; theoretical and empirical findings need to converge to broaden our understanding of this phenomenon. For this purpose, two prominent models have been proposed: the mistiming-model and the lock-key-model. The former states that Wolbachia manipulate sperm of infected males to induce a fatal delay of the male pronucleus during the first embryonic division, but that the bacteria can compensate the delay by slowing down mitosis in fertilized eggs. The latter states that Wolbachia deposit damaging “locks” on sperm DNA of infected males, but can also provide matching “keys” in infected eggs to undo the damage. The lock-key-model, however, needs to assume a large number of locks and keys to explain all existing incompatibility patterns. The mistiming-model requires fewer assumptions but has been contradicted by empirical results. We therefore expand the mistiming-model by one quantitative dimension to create the new, so-called goalkeeper-model. Using a method based on formal logic, we show that both lock-key- and goalkeeper-model are consistent with existing data. Compared to the lock-key-model, however, the goalkeeper-model assumes only two factors and provides an idea of the evolutionary emergence of cytoplasmic incompatibility. Available cytological evidence suggests that the hypothesized second factor of the goalkeeper-model may indeed exist. Finally, we suggest empirical tests that would allow to distinguish between the models. Generalizing our results might prove interesting for the study of the mechanism and evolution of other host-parasite interactions

A Sensitive Search for Supernova Emission Associated with the Extremely Energetic and Nearby GRB 221009A

We report observations of the optical counterpart of the long gamma-ray burst (LGRB) GRB 221009A. Due to the extreme rarity of being both nearby ($z = 0.151$) and highly energetic ($E_{\gamma,\mathrm{iso}} \geq 10^{54}$ erg), GRB 221009A offers a unique opportunity to probe the connection between massive star core collapse and relativistic jet formation across a very broad range of $\gamma$-ray properties. Adopting a phenomenological power-law model for the afterglow and host galaxy estimates from high-resolution Hubble Space Telescope imaging, we use Bayesian model comparison techniques to determine the likelihood of an associated SN contributing excess flux to the optical light curve. Though not conclusive, we find moderate evidence ($K_{\rm{Bayes}}=10^{1.2}$) for the presence of an additional component arising from an associated supernova, SN 2022xiw, and find that it must be substantially fainter ($<$ 67% as bright at the 99% confidence interval) than SN 1998bw. Given the large and uncertain line-of-sight extinction, we attempt to constrain the supernova parameters ($M_{\mathrm{Ni}}$, $M_{\mathrm{ej}}$, and $E_{\mathrm{KE}}$) under several different assumptions with respect to the host galaxy's extinction. We find properties that are broadly consistent with previous GRB-associated SNe: $M_{\rm{Ni}}=0.05$ - $0.25 \, \rm{M_\odot}$, $M_{\rm{ej}}=3.5$ - $11.1 \, \rm{M_\odot}$, and $E_{\rm{KE}} = (1.6$ - $5.2) \times 10^{52} \, \rm{erg}$. We note that these properties are weakly constrained due to the faintness of the supernova with respect to the afterglow and host emission, but we do find a robust upper limit on the $M_{\rm{Ni}}$ of $M_{\rm{Ni}}<0.36\, \rm{M_\odot}$. Given the tremendous range in isotropic gamma-ray energy release exhibited by GRBs (7 orders of magnitude), the SN emission appears to be decoupled from the central engine in these systems.Comment: 18 pages, accepted to ApJL, 4 tables, 5 figures. Updated abstract in Previe

Cooperation under Indirect Reciprocity and Imitative Trust

Indirect reciprocity, a key concept in behavioral experiments and evolutionary game theory, provides a mechanism that allows reciprocal altruism to emerge in a population of self-regarding individuals even when repeated interactions between pairs of actors are unlikely. Recent empirical evidence show that humans typically follow complex assessment strategies involving both reciprocity and social imitation when making cooperative decisions. However, currently, we have no systematic understanding of how imitation, a mechanism that may also generate negative effects via a process of cumulative advantage, affects cooperation when repeated interactions are unlikely or information about a recipient's reputation is unavailable. Here we extend existing evolutionary models, which use an image score for reputation to track how individuals cooperate by contributing resources, by introducing a new imitative-trust score, which tracks whether actors have been the recipients of cooperation in the past. We show that imitative trust can co-exist with indirect reciprocity mechanisms up to a threshold and then cooperation reverses -revealing the elusive nature of cooperation. Moreover, we find that when information about a recipient's reputation is limited, trusting the action of third parties towards her (i.e. imitating) does favor a higher collective cooperation compared to random-trusting and share-alike mechanisms. We believe these results shed new light on the factors favoring social imitation as an adaptive mechanism in populations of cooperating social actors