Biology subjects

Tellier, A.

Publications and source records attributed to Tellier, A..

6 recordsLinked to original sources

bioRxiv2018

Host-parasite coevolution can promote the evolution of seed banking as a bet-hedging strategy

Seed (egg) banking is a common bet-hedging strategy maximizing the fitness of organisms facing environmental unpredictability by the delayed emergence of offspring. Yet, this condition often requires fast and drastic stochastic shifts between good and bad years. We hypothesize that the host seed banking strategy can evolve in response to coevolution with parasites because the coevolutionary cycles promote a gradually changing environment over longer times than seed persistence. We study the evolution of host germination fraction as a quantitative trait using both pairwise competition and multiple mutant competition methods, while the germination locus can be genetically linked or unlinked with the host locus under coevolution. In a gene-for-gene model of coevolution, hosts evolve a seed bank strategy under unstable coevolutionary cycles promoted by moderate to high costs of resistance or strong disease severity. Moreover, when assuming genetic linkage between coevolving and germination loci, the resistant genotype always evolves seed banking in contrast to susceptible hosts. Under a matching-allele interaction, both hosts genotypes exhibit the same seed banking strategy irrespective of the genetic linkage between loci. We suggest host-parasite coevolution as an additional hypothesis for the evolution of seed banking as a temporal bet-hedging strategy.

evolutionary biology↗

bioRxiv2017

The evolutionary history of the current global Ramularia collo-cygni epidemic

Ramularia Leaf Spot (RLS) has emerged as a threat for barley production in many regions of the world. Late appearance of unspecific symptoms caused that Ramularia collo-cygni could only by molecular diagnostics be detected as the causal agent of RLS. Although recent research has shed more light on the biology and genomics of the pathogen, the cause of the recent global spread remains unclear.\n\nTo address urgent questions, especially on the emergence to a major disease, life-cycle, transmission, and quick adaptation to control measures, we de-novo sequenced the genome of R. collo-cygni (urug2 isolate). Additionally, we sequenced fungal RNA from 6 different conditions, which allowed for an improved genome annotation. This resulted in a high quality draft assembly of about 32 Mb, with only 78 scaffolds with an N50 of 2.1 Mb. The overall annotation enabled the prediction of 12.346 high confidence genes. Genomic comparison revealed that R. collo-cygni has significantly diverged from related Dothidiomycetes, including gain and loss of putative effectors, however without obtaining species-specific genome features.\n\nTo evaluate the species-wide genetic diversity, we sequenced the genomes of 19 R. collo-cygni isolates from multiple geographic locations and diverse hosts and mapped sequences to our reference genome. Admixture analyses show that R. collo-cygni is world-wide genetically uniform and that samples do not show a strong clustering on either geographical location or host species. To date, the teleomorph of R. collo-cygni has not been observed. Analysis of linkage disequilibrium shows that in the world-wide sample set there are clear signals of recombination and thus sexual reproduction, however these signals largely disappear when excluding three outliers samples, suggesting that the main global expansion of R. collo-cygni comes from mixed or clonally propagating populations. We further analysed the historic population size (Ne) of R. collo-cygni using Bayesian simulations.\n\nWe discuss how our genomic data and population genetics analysis can help understand the current R. collo-cygni epidemic and provide different hypothesis that are supported by our data. We specifically highlight how recombination, clonal spreading and lack of host-specificity could further support global epidemics of this increasingly recognized plant disease and suggest specific approaches to combat this pathogen.

plant biology↗

bioRxiv2017

A small subset of NLR genes drives local adaptation to pathogens in wild tomato

O_LINucleotide binding site, Leucine-rich repeat Receptors (NLRs), are canonical resistance (R) genes in plants, fungi and animals, functioning as central (helper) and peripheral (sensor) genes in a signalling network. We investigate NLR evolution during the colonisation of novel habitats in a model tomato species, Solanum chilense.\nC_LIO_LIWe used R-gene enrichment sequencing (RENSeq) to obtain polymorphism data at NLRs of 140 plants sampled across 14 populations covering the whole species range. We inferred the past demographic history of habitat colonisation by resequencing whole genomes from three S. chilense plants from three key populations, and performing Approximate Bayesian Computation using data from the 14 populations.\nC_LIO_LIUsing these parameters we simulated the genetic differentiation statistics distribution expected under neutral NLR evolution, and identified small subsets of outlier NLRs exhibiting signatures of selection across populations.\nC_LIO_LINLRs under selection between habitats are more often helper genes, while those showing signatures of adaptation in single populations are more often sensor-NLRs. Thus, centrality in the NLR network does not constrain NLR evolvability, and new mutations in central genes in the network are key for R gene adaptation during colonisation of different habitats.\nC_LI

evolutionary biology↗

bioRxiv2017

Effects of population- and seed bank noise on neutral evolution and efficacy of natural selection

Population genetics models typically consider a fixed population size and a unique selection coefficient. However, population dynamics inherently generate noise in numbers of individuals and selection acts on various components of the individuals fitness. In plant species with seed banks, the size of both the above- and below-ground compartments present noise depending on seed production and the state of the seed bank. We investigate if this noise has consequences on 1) the rate of genetic drift, and 2) the efficacy of selection. We consider four variants of two-allele Moran-type models defined by combinations of presence and absence of noise in above-ground and seed bank compartments. Time scale analysis and dimension reduction methods allow us to reduce the corresponding Fokker-Planck equation to a one-dimensional diffusive Moran model. We first show that if the above-ground noise classically affects the rate of genetic drift, below-ground noise reduces the diversity storage effect of the seed bank. Second, we consider that selection can act on four different components of the plant fitness: plant or seed death rate, seed production or seed germination. Our striking result is that the efficacy of selection for seed death rate or germination rate is reduced by seed bank noise, whereas selection occurring on plant death rate or seed production is not affected. We derive the expected site-frequency spectrum reflecting this heterogeneity in selection efficacy between genes underpinning different plant fitness components. Our results highlight the importance to consider the effect of ecological noise to predict the impact of seed banks on neutral and selective evolution.

evolutionary biology↗

bioRxiv2017

Mutation rates in seeds and seed-banking influence substitution rates across the angiosperm phylogeny

1) BackgroundSeed-banking (the ability to persist in the soil over many generations) is usually considered as a dormant stage where genotypes are \"stored\" as a bet-hedging strategy in response to unpredictable environments. However, seed dormancy may instead have consequences for the integrity of the DNA and generate novel mutations.\n\n2) MethodsWe address this paradox by building phylogenies based on the plastomes and nuclear ITS of species belonging to ten angiosperm clades. In each clade, the substitution rate (branch-length) of a seed-banking species is compared with that of a closely-related non-seed-banking species.\n\n3) ResultsSeed-banking species show as high or higher substitution rates than non-seedbanking species, and therefore mutations occur in dormant seeds at a rate at least as high as in above-ground plants. Moreover, seed born mutations have the same probability to reach fixation as those from above ground. Our results are robust to differences in selection, generation time, and polymorphism.\n\n4) ConclusionsMutations occurring in seeds, and thus seed-banking, affect the population diversity of plant species, and are observable at the macro-evolutionary scale. Our study has consequences for seed storage projects, since the stored seeds are likely to accumulate mutations at a higher rate than previously thought.

evolutionary biology↗

bioRxiv2016

Joint inference of demography and mutation rates from polymorphism data and pedigrees

Inference of demography and mutation rates is of major interest but difficult because genetic data is only informative about the population mutation rate, the product of the effective population size times the mutation rate, and not about these quantities individually. Here we show that this limitation can be overcome by combining genetic data with pedigree information. To successfully use pedigree data, however, important aspects of real populations such as the presence of two sexes, unbalanced sex ratios and overlapping generations have to be taken into account. We present here an extension of the classic Wright-Fisher model accounting for these effects and show that the coalescent process under this model reduces to the classic Kingman coalescent with specific scaling parameters. We further derive the probability of a pedigree under that model and show how pedigree data can thus be used to infer demographic parameters. Finally, we present a computationally efficient inference approach combining pedigree information and genetic data summarized by the site frequency spectrum (SFS) that allows for the joint inference of the mutation rate, sex-specific population sizes and the fraction of overlapping generations. Using simulations we then show that these parameters can be accurately inferred from pedigrees spanning just a few generations, as are available for many species. We finally discuss future possible extensions of the model and inference framework necessary for applications to wild and domesticated species, namely the account for more complex demographies and the uncertainty in assigning pedigree individuals to specific generations.

genetics↗