poolHelper: an R package to help in designing Pool-seq studies

1. Next-generation sequencing of pooled samples (Pool-seq) is an important tool in population genomics and molecular ecology. In Pool-seq, the relative number of reads with an allele reflects the allele frequencies in the sample. However, unequal individual contributions to the pool and sequencing errors can lead to inaccurate allele frequency estimates, influencing downstream analysis. When designing Pool-seq studies, researchers need to decide the pool size (number of individuals) and average depth of coverage (sequencing effort). An efficient sampling design should maximise the accuracy of allele frequency estimates while minimising the sequencing effort. We describe a novel tool to simulate single nucleotide polymorphism (SNP) data using coalescent theory and account for sources of uncertainty in Pool-seq. 2. We introduce an R package, poolHelper, enabling users to simulate Pool-seq data under different combinations of average depth of coverage and pool size, accounting for unequal individual contributions and sequencing errors, modelled by adjustable parameters. The mean absolute error is computed by comparing the sample allele frequencies obtained based on individual genotypes with the frequency estimates obtained with Pool-seq. 3. poolHelper enables users to simulate multiple combinations of pooling errors, average depth of coverage, pool sizes and number of pools to assess how they influence the error of sample allele frequencies and expected heterozygosity. Using simulations under a single population model, we illustrate that increasing the depth of coverage does not necessarily lead to more accurate estimates, reinforcing that finding the best Pool-seq study design is not straightforward. Moreover, we show that simulations can be used to identify different combinations of parameters with similarly low mean absolute errors. This can help users to define an effective sampling design by using those combinations of parameters that minimise the sequencing effort. 4. The poolHelper package provides tools for performing simulations with different combinations of parameters (e.g. pool size, depth of coverage, unequal individual contribution) before sampling and generating data, allowing users to define sampling schemes based on simulations. This allows researchers to focus on the best sampling scheme to answer their research questions. poolHelper is comprehensively documented with examples to guide effective use

Applying genomic approaches to delineate conservation strategies using the freshwater mussel Margaritifera margaritifera in the Iberian Peninsula as a model

Effective conservation actions to counteract the current decline of populations and species require a deep knowledge on their genetic structure. We used Single Nucleotide Polymorphisms (SNPs) to infer the population structure of the highly threatened freshwater pearl mussel Margaritifera margaritifera in the Iberian Peninsula. A total of 130 individuals were collected from 26 locations belonging to 16 basins. We obtained 31,692 SNPs through Genotyping by Sequencing (GBS) and used this dataset to infer population structure. Genetic diversity given as observed heterozygosity was low. Pairwise FST comparisons revealed low levels of genetic differentiation among geographically close populations. Up to 3 major genetic lineages were determined: Atlantic, Cantabrian and Douro. This structure suggests a close co-evolutionary process with brown trout (Salmo trutta), the primordial fish host of this mussel in the studied area. Some sub-basins showed some genetic structuring, whereas in others no intrapopulation differentiation was found. Our results confirm that genetic conservation units do not match individual basins, and that knowledge about the genetic structure is necessary before planning recovery plans that may involve relocation or restocking. The same reasoning should be applied to strictly freshwater species that are sessile or have restricted dispersal abilities and are currently imperiled worldwide.This work was supported by national funds of the Portuguese Foundation for Science and Technology (FCT) through the project MUSSELFLOW (contract PTDC/BIA- EVL/29199/2017) and under the strategic project LA/P/0069/2020 granted to the Associate Laboratory ARNET; and the grant awarded to C.S. Lima (MARE-ISPA/BI/004/2015).Peer reviewe

Charged Dilaton, Energy, Momentum and Angular-Momentum in Teleparallel Theory Equivalent to General Relativity

We apply the energy-momentum tensor to calculate energy, momentum and angular-momentum of two different tetrad fields. This tensor is coordinate independent of the gravitational field established in the Hamiltonian structure of the teleparallel equivalent of general relativity (TEGR). The spacetime of these tetrad fields is the charged dilaton. Our results show that the energy associated with one of these tetrad fields is consistent, while the other one does not show this consistency. Therefore, we use the regularized expression of the gravitational energy-momentum tensor of the TEGR. We investigate the energy within the external event horizon using the definition of the gravitational energy-momentum.Comment: 22 Pages Late

7th Drug hypersensitivity meeting: part two

No abstract availabl