EggLib: processing, analysis and simulation tools for population genetics and genomics

<p>Abstract</p> <p>Background</p> <p>With the considerable growth of available nucleotide sequence data over the last decade, integrated and flexible analytical tools have become a necessity. In particular, in the field of population genetics, there is a strong need for automated and reliable procedures to conduct repeatable and rapid polymorphism analyses, coalescent simulations, data manipulation and estimation of demographic parameters under a variety of scenarios.</p> <p>Results</p> <p>In this context, we present EggLib (Evolutionary Genetics and Genomics Library), a flexible and powerful C++/Python software package providing efficient and easy to use computational tools for sequence data management and extensive population genetic analyses on nucleotide sequence data. EggLib is a multifaceted project involving several integrated modules: an underlying computationally efficient C++ library (which can be used independently in pure C++ applications); two C++ programs; a Python package providing, among other features, a high level Python interface to the C++ library; and the <monospace>egglib </monospace>script which provides direct access to pre-programmed Python applications.</p> <p>Conclusions</p> <p>EggLib has been designed aiming to be both efficient and easy to use. A wide array of methods are implemented, including file format conversion, sequence alignment edition, coalescent simulations, neutrality tests and estimation of demographic parameters by Approximate Bayesian Computation (ABC). Classes implementing different demographic scenarios for ABC analyses can easily be developed by the user and included to the package. EggLib source code is distributed freely under the GNU General Public License (GPL) from its website <url>http://egglib.sourceforge.net/</url> where a full documentation and a manual can also be found and downloaded.</p

De novo sequence assembly and characterization of the floral transcriptome in cross- and self-fertilizing plants

<p>Abstract</p> <p>Background</p> <p>The shift from cross-fertilization to predominant self-fertilization is among the most common evolutionary transitions in the reproductive biology of flowering plants. Increased inbreeding has important consequences for floral morphology, population genetic structure and genome evolution. The transition to selfing is usually characterized by a marked reduction in flower size and the loss of traits involved in pollinator attraction and the avoidance of self-fertilization. Here, we use short-read sequencing to assemble, <it>de novo</it>, the floral transcriptomes of three genotypes of <it>Eichhornia paniculata</it>, including an outcrosser and two genotypes from independently derived selfers, and a single genotype of the sister species <it>E. paradoxa</it>. By sequencing mRNA from tissues sampled at various stages of flower development, our goal was to sequence and assemble the floral transcriptome and identify differential patterns of gene expression.</p> <p>Results</p> <p>Our 24 Mbp assembly resulted in ~27,000 contigs that averaged ~900 bp in length. All four genotypes had highly correlated gene expression, but the three <it>E. paniculata </it>genotypes were more correlated with one another than each was to <it>E. paradoxa</it>. Our analysis identified 269 genes associated with floral development, 22 of which were differentially expressed in selfing lineages relative to the outcrosser. Many of the differentially expressed genes affect floral traits commonly altered in selfing plants and these represent a set of potential candidate genes for investigating the evolution of the selfing syndrome.</p> <p>Conclusions</p> <p>Our study is among the first to demonstrate the use of Illumina short read sequencing for <it>de novo </it>transcriptome assembly in non-model species, and the first to implement this technology for comparing floral transcriptomes in outcrossing and selfing plants.</p

Amount of Information Needed for Model Choice in Approximate Bayesian Computation

Approximate Bayesian Computation (ABC) has become a popular technique in evolutionary genetics for elucidating population structure and history due to its flexibility. The statistical inference framework has benefited from significant progress in recent years. In population genetics, however, its outcome depends heavily on the amount of information in the dataset, whether that be the level of genetic variation or the number of samples and loci. Here we look at the power to reject a simple constant population size coalescent model in favor of a bottleneck model in datasets of varying quality. Not only is this power dependent on the number of samples and loci, but it also depends strongly on the level of nucleotide diversity in the observed dataset. Whilst overall model choice in an ABC setting is fairly powerful and quite conservative with regard to false positives, detecting weaker bottlenecks is problematic in smaller or less genetically diverse datasets and limits the inferences possible in non-model organism where the amount of information regarding the two models is often limited. Our results show it is important to consider these limitations when performing an ABC analysis and that studies should perform simulations based on the size and nature of the dataset in order to fully assess the power of the study

Organisation de la diversité dans les populations autogames (études empiriques chez Medicago truncatula et utilisation pour l'analyse de caractères quantitatifs in natura)

MONTPELLIER-BU Sciences (341722106) / SudocSudocFranceF

EggLib: Evolutionary Genetics and Genomics Library

il s'agit d'un type de produit dont les métadonnées ne correspondent pas aux métadonnées attendues dans les autres types de produit : SOFTWAREEggLib is a C++/Python library and program package for evolutionary genetics and genomics. Main features aresequence data management, sequence polymorphism analysis, coalescent simulations and Approximate BayesianComputation. EggLib is a flexible Python module with a performant underlying C++ library (which can be usedindependently), and allows fast and intuitive development of Python programs and scripts. A number of preprogrammedapplications of EggLib possibilities are available interactively. To get an idea of the possibilitiesoffered by EggLib, see the Manual section

Pedigree-Free Estimates of Heritability in the Wild : Promising Prospects for Selfing Populations

BAPGeapsiCT1Estimating the genetic variance available for traits informs us about a population's ability to evolve in response to novel selective challenges. In selfing species, theory predicts a loss of genetic diversity that could lead to an evolutionary dead-end, but empirical support remains scarce. Genetic variability in a trait is estimated by correlating the phenotypic resemblance with the proportion of the genome that two relatives share identical by descent ('realized relatedness'). The latter is traditionally predicted from pedigrees (Phi(A) : expected value) but can also be estimated using molecular markers (average number of alleles shared). Nevertheless, evolutionary biologists, unlike animal breeders, remain cautious about using marker-based relatedness coefficients to study complex phenotypic traits in populations. In this paper, we review published results comparing five different pedigree-free methods and use simulations to test individual-based models (hereafter called animal models) using marker-based relatedness coefficients, with a special focus on the influence of mating systems. Our literature review confirms that Ritland's regression method is unreliable, but suggests that animal models with marker-based estimates of relatedness and genomic selection are promising and that more testing is required. Our simulations show that using molecular markers instead of pedigrees in animal models seriously worsens the estimation of heritability in outcrossing populations, unless a very large number of loci is available. In selfing populations the results are less biased. More generally, populations with high identity disequilibrium (consanguineous or bottlenecked populations) could be propitious for using marker-based animal models, but are also more likely to deviate from the standard assumptions of quantitative genetics models (non-additive variance)

Effets des interactions entre diversité végétale inter et intraspécifique et communautés microbiennes du sol sur les propriétés de l’écosystème - Candidature à la bourse Phytomic

National audienceLe lien entre diversité et fonctionnement d’un écosystème ainsi que les mécanismes sous-jacents sont très étudiés en génétique des populations et en écologie des communautés et des écosystèmes. La première s’attèle à décrire les effets de la variabilité génétique intraspécifique sur différentes propriétés écosystémiques tandis que la deuxième s’intéresse aux interactions écologiques au niveau interspécifique. Notre objectif est de faire le lien entre ces deux champs disciplinaires par l’étude des effets conjoints d’une mobilisation de la diversité végétale intra et interspécifique et de la diversité microbienne sur les propriétés de l’écosystème. Nous avons mesuré différentes propriétés, liées à la productivité primaire et à l’utilisation des ressources azotées, dans des microcosmes variant pour la diversité spécifique et génotypique du peuplement végétal et impliquant différentes communautés microbiennes telluriques. La combinaison des deux niveaux de diversité du peuplement végétal, inter et intraspécifique, donne lieu à une productivité primaire supérieure et à une teneur en azote minéral du sol inférieure à celles attendues par simple additivité des effets isolés de ces deux niveaux de diversité. Cet effet d’interaction dépend fortement de la communauté microbienne tellurique, en particulier en ce qui concerne la teneur en azote minéral du sol. Nos résultats montrent ainsi l’importance d’intégrer plusieurs composantes et niveaux de diversité dans la compréhension du lien diversité et fonctionnement d’un écosystème et son application dans la gestion des agroécosystèmes

EggLib 3: A python package for population genetics and genomics

International audienceRapid and repeatable polymorphism analyses have become a necessity with the cur-rent amount of genomic data that can be collected in many organisms. Traditionally, such analyses are conducted using a variety of tools in combination, often requiring numerous format translation and manipulation. Here, we present a massively updated version of our previous software package egglib, intended to alleviate such costly and error- prone tinkering with the data. egglib has been streamlined into a python package and thoroughly updated and optimized to accommodate modern-day sized dataset. We show the main characteristics of the package making it a tool of choice to perform population genetics analyses. Once the data are imported (whatever their encoding), they can be filtered, edited, analysed and compared to coalescent simulations very easily and efficiently. Furthermore, the list of diversity and polymorphism statistics that can now be calculated has been greatly expanded. The software and its full docu-mentation are available at https://egglib.org

Genomic consequences of transitions from cross- to self-fertilization on the efficacy of selection in three independently derived selfing plants

International audienceBackground: Transitions from cross- to self-fertilization are associated with increased genetic drift rendering weakly selected mutations effectively neutral. The effect of drift is predicted to reduce selective constraints on amino acid sequences of proteins and relax biased codon usage. We investigated patterns of nucleotide variation to assess the effect of inbreeding on the accumulation of deleterious mutations in three independently evolved selfing plants. Using high-throughput sequencing, we assembled the floral transcriptomes of four individuals of Eichhornia (Pontederiaceae); these included one outcrosser and two independently derived selfers of E. paniculata, and E. paradoxa, a selfing outgroup. The dataset included similar to 8000 loci totalling similar to 3.5 Mb of coding DNA. Results: Tests of selection were consistent with purifying selection constraining evolution of the transcriptome. However, we found an elevation in the proportion of non-synonymous sites that were potentially deleterious in the E. paniculata selfers relative to the outcrosser. Measurements of codon usage in high versus low expression genes demonstrated reduced bias in both E. paniculata selfers. Conclusions: Our findings are consistent with a small reduction in the efficacy of selection on protein sequences associated with transitions to selfing, and reduced selection in selfers on synonymous changes that influence codon usage

Genomic consequences of transitions from cross- to self-fertilization on the efficacy of selection in three independently derived selfing plants

Abstract Background Transitions from cross- to self-fertilization are associated with increased genetic drift rendering weakly selected mutations effectively neutral. The effect of drift is predicted to reduce selective constraints on amino acid sequences of proteins and relax biased codon usage. We investigated patterns of nucleotide variation to assess the effect of inbreeding on the accumulation of deleterious mutations in three independently evolved selfing plants. Using high-throughput sequencing, we assembled the floral transcriptomes of four individuals of Eichhornia (Pontederiaceae); these included one outcrosser and two independently derived selfers of E. paniculata, and E. paradoxa, a selfing outgroup. The dataset included ~8000 loci totalling ~3.5 Mb of coding DNA. Results Tests of selection were consistent with purifying selection constraining evolution of the transcriptome. However, we found an elevation in the proportion of non-synonymous sites that were potentially deleterious in the E. paniculata selfers relative to the outcrosser. Measurements of codon usage in high versus low expression genes demonstrated reduced bias in both E. paniculata selfers. Conclusions Our findings are consistent with a small reduction in the efficacy of selection on protein sequences associated with transitions to selfing, and reduced selection in selfers on synonymous changes that influence codon usage