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in category evolutionary biology
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2,007 downloads evolutionary biology
The distribution of diversity can vary considerably from clade to clade. Attempts to understand these patterns often employ state-dependent speciation and extinction models to determine whether the evolution of a particular novel trait has increased speciation rates and/or decreased their extinction rates. It is still unclear, however, whether these models are uncovering important drivers of diversification, or whether they are simply pointing to more complex patterns involving many unmeasured and co-distributed factors. Here we describe an extension to the popular state-dependent speciation and extinction models that specifically accounts for the presence of unmeasured factors that could impact diversification rates estimated for the states of any observed trait, addressing at least one major criticism of BiSSE methods. Specifically, our model, which we refer to as HiSSE (Hidden-State Speciation and Extinction), assumes that related to each observed state in the model are "hidden" states that exhibit potentially distinct diversification dynamics and transition rates than the observed states in isolation. We also demonstrate how our model can be used as character-independent diversification (CID) models that allow for a complex diversification process that is independent of the evolution of a character. Under rigorous simulation tests and when applied to empirical data, we find that HiSSE performs reasonably well, and can at least detect net diversification rate differences between observed and hidden states and detect when diversification rate differences do not correlate with the observed states. We discuss the remaining issues with state-dependent speciation and extinction models in general, and the important ways in which HiSSE provides a more nuanced understanding of trait-dependent diversification.
2,002 downloads evolutionary biology
We introduce ABLE (Approximate Blockwise Likelihood Estimation), a novel composite likelihood framework based on a recently introduced summary of sequence variation: the blockwise site frequency spectrum (bSFS). This simulation-based framework uses the the frequencies of bSFS configurations to jointly model demographic history and recombination and is explicitly designed to make inference using multiple whole genomes or genome-wide multi-locus data (e.g. RADSeq) catering to the needs of researchers studying model or non-model organisms respectively. The flexible nature of our method further allows for arbitrarily complex population histories using unphased and unpolarized whole genome sequences. In silico experiments demonstrate accurate parameter estimates across a range of divergence models with increasing complexity, and as a proof of principle, we infer the demographic history of the two species of orangutan from multiple genome sequences (over 160 Mbp in length) from each species. Our results indicate that the two orangutan species split approximately 650-950 thousand years ago but experienced a pulse of secondary contact much more recently, most likely during a period of low sea-level South East Asia (~300,000 years ago). Unlike previous analyses we can reject a history of continuous gene flow and co-estimate genome-wide recombination. ABLE is available for download at https://github.com/champost/ABLE.
1,997 downloads evolutionary biology
Inference for population genetics models is hindered by computationally intractable likelihoods. While this issue is tackled by likelihood-free methods, these approaches typically rely on hand-crafted summary statistics of the data. In complex settings, designing and selecting suitable summary statistics is problematic and results are very sensitive to such choices. In this paper, we learn the first exchangeable feature representation for population genetic data to work directly with genotype data. This is achieved by means of a novel Bayesian likelihood-free inference framework, where a permutation-invariant convolutional neural network learns the inverse functional relationship from the data to the posterior. We leverage access to scientific simulators to learn such likelihood-free function mappings, and establish a general framework for inference in a variety of simulation-based tasks. We demonstrate the power of our method on the recombination hotspot testing problem, outperforming the state-of-the-art.
1,983 downloads evolutionary biology
Recombination is a process that unlinks neighbouring loci allowing for independent evolutionary trajectories within genomes of many organisms. If not properly accounted for, recombination can compromise many evolutionary analyses. In addition, when dealing with organisms that are not obligately sexually reproducing, recombination gives insight into the rate at which distinct genetic lineages come into contact. Since June, 2012, Middle East respiratory syndrome coronavirus (MERS-CoV) has caused 1106 laboratory-confirmed infections, with 421 MERS-CoV associated deaths as of April 16, 2015. Although bats are considered as the likely ultimate source of zoonotic betacoronaviruses, dromedary camels have been consistently implicated as the source of current human infections in the Middle East. In this paper we use phylogenetic methods and simulations to show that MERS-CoV genome has likely undergone numerous recombinations recently. Recombination in MERS-CoV implies frequent co-infection with distinct lineages of MERS-CoV, probably in camels given the current understanding of MERS-CoV epidemiology.
1,958 downloads evolutionary biology
Experiments show that evolutionary fitness landscapes can have a rich combinatorial structure due to epistasis. For some landscapes, this structure can produce a computational constraint that prevents evolution from finding local fitness optima -- thus overturning the traditional assumption that local fitness peaks can always be reached quickly if no other evolutionary forces challenge natural selection. Here, I introduce a distinction between easy landscapes of traditional theory where local fitness peaks can be found in a moderate number of steps and hard landscapes where finding local optima requires an infeasible amount of time. Hard examples exist even among landscapes with no reciprocal sign epistasis; on these semi-smooth fitness landscapes, strong selection weak mutation dynamics cannot find the unique peak in polynomial time. More generally, on hard rugged fitness landscapes that include reciprocal sign epistasis, no evolutionary dynamics -- even ones that do not follow adaptive paths -- can find a local fitness optimum quickly. Moreover, on hard landscapes, the fitness advantage of nearby mutants cannot drop off exponentially fast but has to follow a power-law that long term evolution experiments have associated with unbounded growth in fitness. Thus, the constraint of computational complexity enables open-ended evolution on finite landscapes. Knowing this constraint allows us to use the tools of theoretical computer science and combinatorial optimization to characterize the fitness landscapes that we expect to see in nature. I present candidates for hard landscapes at scales from single genes, to microbes, to complex organisms with costly learning (Baldwin effect) or maintained cooperation (Hankshaw effect). Just how ubiquitous hard landscapes (and the corresponding ultimate constraint on evolution) are in nature becomes an open empirical question.
1,946 downloads evolutionary biology
Methods for inferring population structure from genetic information traditionally assume samples are contemporary. Yet, the increasing availability of ancient DNA sequences begs revision of this paradigm. We present Dystruct (Dynamic Structure), a framework and toolbox for inference of shared ancestry from data that include ancient DNA. By explicitly modeling population history and genetic drift as a time-series, Dystruct more accurately and realistically discovers shared ancestry from ancient and contemporary samples. Formally, we use a normal approximation of drift, which allows a novel, efficient algorithm for optimizing model parameters using stochastic variational inference. We show that Dystruct outperforms the state of the art when individuals are sampled over time, as is common in ancient DNA datasets. We further demonstrate the utility of our method on a dataset of 92 ancient samples alongside 1941 modern ones genotyped at 222755 loci. Our model tends to present modern samples as the mixtures of ancestral populations they really are, rather than the artifactual converse of presenting ancestral samples as mixtures of contemporary groups.
1,942 downloads evolutionary biology
Roberto Amato, Olivo Miotto, Charles Woodrow, Jacob Almagro-Garcia, Ipsita Sinha, Susana Campino, Daniel Mead, Eleanor Drury, Mihir Kekre, Mandy Sanders, Alfred Amambua-Ngwa, Chanaki Amaratunga, Lucas Amenga-Etego, Tim J C Anderson, Voahangy Andrianaranjaka, Tobias Apinjoh, Elizabeth Ashley, Sarah Auburn, Gordon A Awandare, Vito Baraka, Alyssa Barry, Maciej F. Boni, Steffen Borrmann, Teun Bousema, Oralee Branch, Peter C Bull, Kesinee Chotivanich, David J Conway, Alister Craig, Nicholas P Day, Abdoulaye Djimdé, Christiane Dolecek, Arjen M. Dondorp, Chris Drakeley, Patrick Duffy, Diego F Echeverri-Garcia, Thomas G Egwang, Rick M. Fairhurst, Abul Faiz, Caterina I Fanello, Tran Tinh Hien, Abraham Hodgson, Mallika Imwong, Deus Ishengoma, Pharath Lim, Chanthap Lon, Jutta Marfurt, Kevin Marsh, Mayfong Mayxay, Victor Mobegi, Olugbenga Mokuolu, Jacqui Montgomery, Ivo Mueller, Myat Phone Kyaw, Paul N Newton, Francois Nosten, Rintis Noviyanti, Alexis Nzila, Harold Ocholla, Abraham Oduro, Marie Onyamboko, Jean-Bosco Ouedraogo, Aung Pyae Phyo, Christopher V Plowe, Ric N Price, Sasithon Pukrittayakamee, Milijaona Randrianarivelojosia, Pascal Ringwald, Lastenia Ruiz, David Saunders, Alex Shayo, Peter Siba, Shannon Takala-Harrison, Thuy-Nhien Nguyen Thanh, Vandana Thathy, Federica Verra, Nicholas J. White, Ye Htut, Victoria J Cornelius, Rachel Giacomantonio, Dawn Muddyman, Christa Henrichs, Cinzia Malangone, Dushyanth Jyothi, Richard D. Pearson, Julian C Rayner, Gilean McVean, Kirk Rockett, Alistair Miles, Paul Vauterin, Ben Jeffery, Magnus Manske, Jim Stalker, Bronwyn MacInnis, Dominic P Kwiatkowski, MalariaGEN Plasmodium falciparum Community Project
Artemisinin resistant Plasmodium falciparum is advancing across Southeast Asia in a soft selective sweep involving at least 20 independent kelch13 mutations. In a large global survey, we find that kelch13 mutations which cause resistance in Southeast Asia are present at low frequency in Africa. We show that African kelch13 mutations have originated locally, and that kelch13 shows a normal variation pattern relative to other genes in Africa, whereas in Southeast Asia there is a great excess of non‐synonymous mutations, many of which cause radical amino‐acid changes. Thus, kelch13 is not currently undergoing strong selection in Africa, despite a deep reservoir of standing variation that could potentially allow resistance to emerge rapidly. The practical implications are that public health surveillance for artemisinin resistance should not rely on kelch13 data alone, and interventions to prevent resistance must account for local evolutionary conditions, shown by genomic epidemiology to differ greatly between geographical regions.
1,931 downloads evolutionary biology
Growing demands for aquatic sources of animal proteins have attracted significant investments in aquaculture research in recent years. The crustacean aquaculture industry has undergone substantial growth to accommodate a rising global demand, however such large-scale production is susceptible to pathogen-mediated destruction. It is clear that a thorough understanding of the crustacean innate immune system is imperative for future research into combating current and future pathogens of the main food crop species. Through a comparative genomics approach utilising extant data from 55 species, we describe the innate immune system of crustaceans from the Malacostraca class. We identify 7407 malacostracan genes from 39 gene families implicated in different aspects of host defence and demonstrate dynamic evolution of innate immunity components within this group. Malacostracans have achieved flexibility in recognising infectious agents through divergent evolution and expansion of pathogen recognition receptors genes. Antiviral RNAi, Toll and JAK-STAT signal transduction pathways have remained conserved within Malacostraca, although the Imd pathway appears to lack several key components. Immune effectors such as the antimicrobial peptides (AMPs) have unique evolutionary profiles, with many malacostracan AMPs not found in other arthropod groups. Lastly, we describe four putative novel immune gene families, characterised by distinct protein domains, potentially representing important evolutionary novelties of the malacostracan immune system.
1,924 downloads evolutionary biology
There is accumulating evidence that some genes have originated de novo from previously non-coding genomic sequences. However, the processes underlying de novo gene birth are still enigmatic. In particular, the appearance of a new functional protein seems highly improbable unless there is already a pool of neutrally evolving peptides that can at some point acquire new functions. Here we show for the first time that such peptides do not only exist but that they are prevalent among the translation products of mouse genes that lack homologues in rat and human. The data suggests that the translation of these peptides is due to the chance occurrence of open reading frames with a favorable codon composition. Our approach combines ribosome profiling experiments, proteomics data and non-synonymous and synonymous nucleotide polymorphism analysis. We propose that effectively neutral processes involving the expression of thousands of transcripts all the way down to proteins provide a basis for de novo gene evolution.
1,912 downloads evolutionary biology
Aida Andrades Valtueña, Alissa Mittnik, Felix M. Key, Wolfgang Haak, Raili Allmäe, Andrej Belinskij, Mantas Daubaras, Michal Feldman, Rimantas Jankauskas, Ivor Janković, Ken Massy, Mario Novak, Saskia Pfrengle, Sabine Reinhold, Mario Šlaus, Maria A. Spyrou, Anna Szecsenyi-Nagy, Mari Tõrv, Svend Hansen, Kirsten I. Bos, Philipp W. Stockhammer, Alexander Herbig, Johannes Krause
Molecular signatures of Yersinia pestis were recently identified in prehistoric Eurasian individuals, thus suggesting Y. pestis caused some form of disease in humans prior to the first historically documented pandemic. Here, we present six new Y. pestis genomes spanning from the European Late Neolithic to the Bronze Age (LNBA) dating from 4,800 to 3,700 BP. We show that all currently investigated LNBA strains form a single genetic clade in the Y. pestis phylogeny that appears to be extinct. Interpreting our data within the context of recent ancient human genomic evidence, which suggests an increase in human mobility during the LNBA, we propose a possible scenario for the spread of Y. pestis during the LNBA: Y. pestis may have entered Europe from Central Eurasia during an expansion of steppe people, persisted within Europe until the mid Bronze Age, and moved back towards Central Eurasia in parallel with subsequent human population movements.
1,896 downloads evolutionary biology
Estimates of microbial fitness from growth curves are inaccurate. Rather, competition experiments are necessary for accurate estimation. But competition experiments require unique markers and are difficult to perform with isolates derived from a common ancestor or non-model organisms. Here we describe a new approach for predicting relative growth of microbes in a mixed culture utilizing mono- and mixed culture growth curve data. We validated this approach using growth curve and competition experiments with E. coli. Our approach provides an effective way to predict growth in a mixed culture and infer relative fitness. Furthermore, by integrating several growth phases, it provides an ecological interpretation for microbial fitness.
1,887 downloads evolutionary biology
A common belief among human life history researchers is that "harsher" environments - i.e., those with higher mortality rates and resource stress - select for "fast" life histories, i.e. earlier reproduction and faster senescence. I show that these "harsh environments, fast life histories" - or HEFLH - hypotheses are poorly supported by evolutionary theory. First, I use a simple model to show that effects of environmental harshness on life history evolution are incredibly diverse. In particular, small changes in basic but poorly understood variables - e.g., whether and how population density affects vital rates - can cause selection to favor very different life histories. Furthermore, I show that almost all life history theory used to justify HEFLH hypotheses is misapplied in the first place. The reason is that HEFLH hypotheses usually treat plastic responses to heterogeneous environmental conditions within a population, whereas the theory used to justify such hypotheses treat genetic responses to environmental changes across an entire population. Counter-intuitively, the predictions of the former do not generally apply to the latter: the optimal response to a harsh environment within a large heterogeneous environment is not necessarily the optimal strategy of a population uniformly inhabiting the same harsh environment. I discuss these theoretical results in light of the current state of empirical research.
1,882 downloads evolutionary biology
In a recent article entitled On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE, Graur et al. dismantle ENCODEs evidence and conclusion that 80% of the human genome is functional. However, the article by Graur et al. contains assumptions and statements that are questionable. Primarily, the authors limit their evaluation of DNAs biological functions to informational roles, sidestepping putative non-informational functions. Here, I bring forward an old hypothesis on the evolution of genome size and on the role of so called junk DNA (jDNA), which might explain C-value enigma. According to this hypothesis, the jDNA functions as a defense mechanism against insertion mutagenesis by endogenous and exogenous inserting elements such as retroviruses, thereby protecting informational DNA sequences from inactivation or alteration of their expression. Notably, this model couples the mechanisms and the selective forces responsible for the origin of jDNA with its putative protective biological function, which represents a classic case of fighting fire with fire. One of the key tenets of this theory is that in humans and many other species, jDNAs serves as a protective mechanism against insertional oncogenic transformation. As an adaptive defense mechanism, the amount of protective DNA varies from one species to another based on the rate of its origin, insertional mutagenesis activity, and evolutionary constraints on genome size.
1,873 downloads evolutionary biology
It has been widely acknowledged that many phenomena in ecology and evolution depend on spatial and temporal scale. However, important patterns and processes may also vary across the phylogeny and depend on phylogenetic scale. Though phylogenetic scale has been implicitly considered in some previous studies, it has never been formally conceptualized and its potential remains unexplored. Here, we develop the concept of phylogenetic scale and, building on previous work in the field, we introduce phylogenetic grain and extent, phylogenetic scaling and the domains of phylogenetic scale. We use examples from published research to demonstrate how phylogenetic scale has been considered so far and illustrate how it can inform, and possibly resolve, some of the longstanding controversies in evolutionary biology, community ecology, biogeography and macroecology. To promote the concept of phylogenetic scale empirically, we propose methodological guidelines for its treatment.
1,871 downloads evolutionary biology
Coding and non-coding mutations in DNA contribute significantly to phenotypic variability during evolution. However, less is known about the role of epigenetics in this process. Although previous studies have identified eye development genes associated with the loss of eyes phenotype in the Pachon blind cave morph of the Mexican tetra Astyanax mexicanus1-6, no inactivating mutations have been found in any of these genes2,3,7-10. Here we show that excess DNA methylation-based epigenetic silencing promotes eye degeneration in blind cave Astyanax mexicanus. By performing parallel analyses in Astyanax mexicanus cave and surface morphs and in the zebrafish Danio rerio, we have discovered that DNA methylation mediates eye-specific gene repression and globally regulates early eye development. The most significantly hypermethylated and down-regulated genes in the cave morph are also linked to human eye disorders, suggesting the function of these genes is conserved across the vertebrates. Our results show that changes in DNA methylation-based gene repression can serve as an important molecular mechanism generating phenotypic diversity during development and evolution.
1,849 downloads evolutionary biology
Background and Rationale Post-marital residence patterns refer to where a couple lives after marriage, such as near or with husband's kin (patrilocality) or wife's kin (matrilocality). These patterns influence other aspects of social organization and behavior, and potentially reveal key parts of human nature. Since the 1860s, anthropologists have sought to characterize prehistoric hunter-gatherers' post-marital residence patterns by extrapolating from modern hunter-gatherers' and chimpanzees' behavior. For many reasons, these extrapolations are invalid. I summarized direct evidence of residence patterns from prehistoric hunter-gatherers' remains. Methods I conducted a systematic review of strontium isotope and mitochondrial DNA (mtDNA) studies of prehistoric hunter-gatherers and extinct hominins. I also carried out a systematic review of the reliability of classifying prehistoric hunter-gatherer individuals by sex. To evaluate assumptions underlying my analyses of residence patterns, I reviewed the ethnographic literature on hunter-gatherers' mortuary practices as represented in the eHRAF World Cultures database. Results The archaeologic sites included in my review represent every inhabited continent except Australia, and their dates span almost the last 10,000 years. In the strontium isotope studies, most adults of both sexes were local, and women were slightly more likely to be local than men. Within sites, women and men had similar mtDNA distributions. Women in neighboring, contemporaneous communities had somewhat distinct mtDNA distributions from each other, while the mtDNA distributions of men in the different communities were less distinguishable. The statistical uncertainties for most summaries are fairly large. Taken together, the results indicate the burial communities were mostly endogamous and that exogamous marriages strained toward matrilocality. The very limited research on extinct hominins' residence patterns is consistent with these findings. In addition, there was only a moderate correspondence between morphologic and genetic estimates of sex in adult prehistoric hunter-gatherer individuals. When I corrected for this measurement error or relied on genetic estimates of sex only, the post-marital residence pattern results shifted in the direction of greater matrilocal tendencies. Modern hunter-gatherers' burial practices were consonant with the assumptions underlying my analyses. Conclusions Direct evidence from prehistoric hunter-gatherers' remains indicates very different post-marital residence patterns than those extrapolated from modern hunter-gatherers' and chimpanzees' behavior. In prehistoric hunter-gatherer settings, endogamy may be the outcome of humans' long-term mating preferences. Endogamy may have inhibited bacterial sexually transmitted diseases in prehistory and enabled the evolution of altruism in humans.
1,848 downloads evolutionary biology
Even if a species' phenotype remains unchanged over evolutionary time, the underlying mechanism may have changed, as distinct molecular pathways can realize identical phenotypes. Here we use quantitative genetics and linear system theory to study how a gene network underlying a conserved phenotype evolves, as the genetic drift of small mutational changes to these molecular pathways cause a population to explore the set of mechanisms with identical phenotypes. To do this, we model an organism's internal state as a linear system of differential equations for which the environment provides input and the phenotype is the output, in which context there exists an exact characterization of the set of all mechanisms that give the same input-output relationship. This characterization implies that selectively neutral directions in genotype space should be common and that the evolutionary exploration of these distinct but equivalent mechanisms can lead to the reproductive incompatibility of independently evolving populations. This evolutionary exploration, or system drift, proceeds at a rate proportional to the amount of intrapopulation genetic variation divided by the effective population size (Ne). At biologically reasonable parameter values this process can lead to substantial interpopulation incompatibility, and thus speciation, in fewer than Ne generations. This model also naturally predicts Haldane's rule, thus providing another possible explanation of why heterogametic hybrids tend to be disrupted more often than homogametes during the early stages of speciation.
1,844 downloads evolutionary biology
Background: Dogs (Canis lupus familiaris) were domesticated from gray wolves between 10-40 kya in Eurasia, yet details surrounding the process of domestication remain unclear. The vast array of phenotypes exhibited by dogs mirror other domesticated animal species, a phenomenon known as the Domestication Syndrome. Here, we use signatures persisting in the dog genome to identify genes and pathways altered by the intensive selective pressures of domestication. Results: We identified 246 candidate domestication regions containing 10.8Mb of genome sequence and 178 genes through whole-genome SNP analysis of 43 globally distributed village dogs and 10 wolves. Comparisons with ancient dog genomes suggest that these regions reflect signatures of domestication rather than breed formation. The strongest hit is located in the Retinoic Acid-Induced 1 (RAI1) gene, mutations of which cause Smith-Magenis syndrome. The identified regions contain a significant enrichment of genes linked to neural crest cell migration, differentiation and development. Read depth analysis suggests that copy number variation played a minor role in dog domestication. Conclusion: Our results indicate that phenotypes distinguishing domesticated dogs from wolves, such as tameness, smaller jaws, floppy ears, and diminished craniofacial development, are determined by genes which act early in embryogenesis. These differences are all phenotypes of the Domestication Syndrome, which can be explained by decreases in neural crest cells at these sites. We propose that initial selection during early dog domestication was for behavior, a trait also influenced by genes which act in the neural crest, which secondarily gave rise to the phenotypes of modern dogs.
1,823 downloads evolutionary biology
Gire et al. (Science 345:1369-1372, 2014) analyzed 81 complete genomes sampled from the 2014 Zaire ebolavirus (EBOV) outbreak and reported "rapid accumulation of [...] genetic variation" and a substitution rate that was "roughly twice as high within the 2014 outbreak as between outbreaks." These findings have received widespread attention, and many have perceived Gire et al.'s results as implying rapid adaptation of EBOV to humans during the current outbreak. Here, we argue that, on the contrary, sequence divergence in EBOV is rather limited, and that the currently available data contain no robust signal of particularly rapid evolution or adaptation to humans. The doubled substitution rate can be attributed entirely to the application of a molecular-clock model to a population of sequences with minimal divergence and segregating polymorphisms. Our results highlight how subtle technical aspects of sophisticated evolutionary analysis methods may result in highly-publicized, misconstrued statements about an ongoing public health crisis.
1,823 downloads evolutionary biology
Transcriptome-enabled phylogenetic analyses have dramatically improved our understanding of metazoan phylogeny in recent years, although several important questions remain. The branching order near the base of the tree is one such outstanding issue. To address this question we assemble a novel data set comprised of 1,080 orthologous loci derived from 36 publicly available genomes and dissect the phylogenetic signal present in each individual partition. The size of this data set allows for a closer look at the potential biases and sources of non-phylogenetic signal. We assessed a range of measures for each data partition including information content, saturation, rate of evolution, long-branch score, and taxon occupancy and explored how each of these characteristics impacts phylogeny estimation. We then used these data to prepare a reduced set of partitions that fit an optimal set of criteria and are amenable to the most appropriate and computationally intensive analyses using site-heterogeneous models of sequence evolution. We also employed several strategies to examine the potential for long-branch attraction to bias our inferences. All of our analyses support Ctenophora as the sister lineage to other Metazoa, although support for this relationship varies among analyses. We find no support for the traditional view uniting the ctenophores and Cnidaria (jellies, anemones, corals, and kin). We also examine phylogenetic placement of myriapods (centipedes and millipedes) and find it more sensitive to the type of analysis and data used. Our study provides a workflow for minimizing systematic bias in whole genome-based phylogenetic analyses.
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