JMATING: a software for the analysis of sexual selection and sexual isolation effects from mating frequency data

BACKGROUND: Many different sexual isolation and sexual selection statistics have been proposed in the past. However, there is no available software that implements all these statistical estimators and their corresponding tests for the study of mating behaviour. RESULTS: JMATING is an easy-to-use program developed in Java for the analysis of mating frequency data to study sexual selection and sexual isolation effects from laboratory experiments as well as descriptive studies accomplished in the wild. The software allows the re-organization of the data previous to the analysis, the estimation of the most important estimators, and a battery of complementary statistical tests. CONCLUSION: JMATING is the first complete and versatile software for the analyses of mating frequency data. It is available at and requires the Java runtime environment

‘SGoFicance Trace’: Assessing Significance in High Dimensional Testing Problems

Recently, an exact binomial test called SGoF (Sequential Goodness-of-Fit) has been introduced as a new method for handling high dimensional testing problems. SGoF looks for statistical significance when comparing the amount of null hypotheses individually rejected at level γ = 0.05 with the expected amount under the intersection null, and then proceeds to declare a number of effects accordingly. SGoF detects an increasing proportion of true effects with the number of tests, unlike other methods for which the opposite is true. It is worth mentioning that the choice γ = 0.05 is not essential to the SGoF procedure, and more power may be reached at other values of γ depending on the situation. In this paper we enhance the possibilities of SGoF by letting the γ vary on the whole interval (0,1). In this way, we introduce the ‘SGoFicance Trace’ (from SGoF's significance trace), a graphical complement to SGoF which can help to make decisions in multiple-testing problems. A script has been written for the computation in R of the SGoFicance Trace. This script is available from the web site http://webs.uvigo.es/acraaj/SGoFicance.htm

Evaluation of Existing Methods for High-Order Epistasis Detection

[Abstract] Finding epistatic interactions among loci when expressing a phenotype is a widely employed strategy to understand the genetic architecture of complex traits in GWAS. The abundance of methods dedicated to the same purpose, however, makes it increasingly difficult for scientists to decide which method is more suitable for their studies. This work compares the different epistasis detection methods published during the last decade in terms of runtime, detection power and type I error rate, with a special emphasis on high-order interactions. Results show that in terms of detection power, the only methods that perform well across all experiments are the exhaustive methods, although their computational cost may be prohibitive in large-scale studies. Regarding non-exhaustive methods, not one could consistently find epistasis interactions when marginal effects are absent. If marginal effects are present, there are methods that perform well for high-order interactions, such as BADTrees, FDHE-IW, SingleMI or SNPHarvester. As for false-positive control, only SNPHarvester, FDHE-IW and DCHE show good results. The study concludes that there is no single epistasis detection method to recommend in all scenarios. Authors should prioritize exhaustive methods when sufficient computational resources are available considering the data set size, and resort to non-exhaustive methods when the analysis time is prohibitive.10.13039/501100010801-Xunta de Galicia (Grant Number: ED431C2016-037, ED431C2017/04 and ED431G2019/01) 10.13039/501100003176-Ministerio de Educacion Cultura y Deporte (Grant Number: FPU16/01333) 10.13039/501100003329-Ministerio de Economia y Competitividad (Grant Number: CGL2016-75482-P, PID2019-104184RB-I00, AEI/FEDER/EU, 10.13039/50110 and TIN2016-75845-P)Xunta de Galicia; ED431C2016-037Xunta de Galicia; ED431G2019/01Xunta de Galicia; ED431C 2017/0

Toxo: A Library for Calculating Penetrance Tables of High-Order Epistasis Models

[Abstract] Background Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which contains the probability of expressing the phenotype under study given a particular allele combination. Available simulators can only create penetrance tables for well-known epistasis models involving a small number of genes and under a large number of limitations. Results Toxo is a MATLAB library designed to calculate penetrance tables of epistasis models of any interaction order which resemble real data more closely. The user specifies the desired heritability (or prevalence) and the program maximizes the table’s prevalence (or heritability) according to the input epistatic model boundaries. Conclusions Toxo extends the capabilities of existing simulators that define epistasis using penetrance tables. These tables can be directly used as input for software simulators such as GAMETES so that they are able to generate data samples with larger interactions and more realistic prevalences/heritabilities.This research was supported by the Ministry of Economy and Competitiveness of Spain (CGL2016-75482-P), the Ministry of Economy and Competitiveness of Spain and FEDER funds of the EU (TIN2016-75845-P), the Xunta de Galicia (Grupo de Referencia Competitiva, ED431C2016-037), the Xunta de Galicia and FEDER funds of the EU (Centro de Investigación de Galicia accreditation 2019-2022, ref. ED431G2019/01), Consolidation Program of Competitive Research (ED431C 2017/04) and the FPU Program of the Ministry of Education of Spain (FPU16/01333)Xunta de Galicia; ED431C2016-037Xunta de Galicia; ED431G2019/01Xunta de Galicia; ED431C 2017/0

Assessing Significance in High-Throughput Experiments by Sequential Goodness of Fit and q-Value Estimation

We developed a new multiple hypothesis testing adjustment called SGoF+ implemented as a sequential goodness of fit metatest which is a modification of a previous algorithm, SGoF, taking advantage of the information of the distribution of p-values in order to fix the rejection region. The new method uses a discriminant rule based on the maximum distance between the uniform distribution of p-values and the observed one, to set the null for a binomial test. This new approach shows a better power/pFDR ratio than SGoF. In fact SGoF+ automatically sets the threshold leading to the maximum power and the minimum false non-discovery rate inside the SGoF' family of algorithms. Additionally, we suggest combining the information provided by SGoF+ with the estimate of the FDR that has been committed when rejecting a given set of nulls. We study different positive false discovery rate, pFDR, estimation methods to combine q-value estimates jointly with the information provided by the SGoF+ method. Simulations suggest that the combination of SGoF+ metatest with the q-value information is an interesting strategy to deal with multiple testing issues. These techniques are provided in the latest version of the SGoF+ software freely available at http://webs.uvigo.es/acraaj/SGoF.htm

Exchangeable Self-Assembled Lanthanide Antennas for PLIM Microscopy

This is the published manuscript version of the following manuscript: Exchangeable Self-Assembled Lanthanide Antennas for PLIM Microscopy, Angew. Chem. Int. Ed. 2023, e202314595 doi: https://doi.org/10.1002/anie.202314595 This article may be used for non-commercial purposes in accordance with Wiley Sharing Policies. Supplementary Materials accompanying this article can be found on-line at the publisher’s site.Lanthanides have unique photoluminescence (PL) emission properties, including very long PL life- times. This makes them ideal for biological imaging applications, especially using PL lifetime imaging micro- scopy (PLIM). PLIM is an inherently multidimensional technique with exceptional advantages for quantitative biological imaging. Unfortunately, due to the required prolonged acquisitions times, photobleaching of lantha- nide PL emission currently constitutes one of the main drawbacks of PLIM. In this study, we report a small aqueous-soluble, lanthanide antenna, 8-methoxy-2-oxo- 1,2,4,5-tetrahydrocyclopenta[de]quinoline-3-phosphonic acid, PAnt, specifically designed to dynamically interact with lanthanide ions, serving as exchangeable dye aimed at mitigating photobleaching in PLIM microscopy in cellulo. Thus, self-assembled lanthanide complexes that may be photobleached during image acquisition are continuously replenished by intact lanthanide antennas from a large reservoir. Remarkably, our self-assembled lanthanide complex clearly demonstrated a significant reduction of PL photobleaching when compared to well- established lanthanide cryptates, used for bioimaging. This concept of exchangeable lanthanide antennas opens new possibilities for quantitative PLIM bioimaging.Grant PID2020-114256RB-I00 funded by AEI/10.13039/501100011033Grant PID2019- 104366RB-C22 funded by AEI/10.13039/501100011033/ FEDER “Una manera de hacer Europa”Grants P21_00212, A-FQM-386-UGR20 and 2021/00627/001-FEDER_UJA_ 2020 funded by FEDER/Junta de Andalucía-Consejería de Transformación Económica, Industria, Conocimiento y UniversidadesCSIC grant 202180E073Acción 1 from Universidad de JaénFunding for open access charge: Universidad de Granada/CBUASpanish Ministerio de Educación y Formación Profesional for the FPU Ph.D. scholarshi

La importancia de la planificación del talento humano en la empresa de alimentos campo norte de la ciudad de Bogotá

no aplicaEl presente trabajo se realiza un análisis del proceso de selección, vinculación y contratación de personal, para llevar a cabo una buena planificación de talento humano en la organización Alimentos Campo Norte ubicada en la ciudad de Bogotá. Los procesos administrativos del talento humano utilizado la empresa seleccionada debe conllevar al fomento de la eficiencia de las actividades administrativas y productivas que le permitan estar a la vanguardia de la demanda que enmarca los nuevos retos económicos internacionales. En consecuencia, se ha visto la necesidad de realizar un análisis del proceso de recurso humano a la empresa Alimentos Campo Norte ubicada en la ciudad de Bogotá, que permita desarrollar una propuesta de desarrollo de talento humano tales como planeación, reclutamiento, selección, contratación que se llevan cabo dentro de la empresa. Como aprendizaje personal quedara la posibilidad de poner en práctica los conocimientos adquiridos con este diplomado.The present work is an analysis of the process of selection, linking and hiring of personnel, to carry out a good planning of human talent in the organization Alimentos Campo located in the city of Bogotá. The administrative processes of the human talent used by the selected company must lead to the promotion of the efficiency of the administrative and productive activities that allow it to be at the forefront of the demand that frames the new international economic challenges. Consequently, it has been seen the need to carry out an analysis of the human resource process at the company Alimentos Campo Norte located in the city of Bogotá, which allows the development of a human talent development proposal such as planning, recruitment, selection, hiring that are carried out within the company. As personal learning, there will be the possibility of putting into practice the knowledge acquired with this diploma

GENOMEPOP: A program to simulate genomes in populations

<p>Abstract</p> <p>Background</p> <p>There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using backward or forward strategies. Backward simulations, also called coalescent-based simulations, are computationally efficient. The reason is that they are based on the history of lineages with surviving offspring in the current population. On the contrary, forward simulations are less efficient because the entire population is simulated from past to present. However, the coalescent framework imposes some limitations that forward simulation does not. Hence, there is an increasing interest in forward population genetic simulation and efficient new tools have been developed recently. Software tools that allow efficient simulation of large DNA fragments under complex evolutionary models will be very helpful when trying to better understand the trace left on the DNA by the different interacting evolutionary forces. Here I will introduce GenomePop, a forward simulation program that fulfills the above requirements. The use of the program is demonstrated by studying the impact of intracodon recombination on global and site-specific <it>dN/dS </it>estimation.</p> <p>Results</p> <p>I have developed algorithms and written software to efficiently simulate, forward in time, different Markovian nucleotide or codon models of DNA mutation. Such models can be combined with recombination, at inter and intra codon levels, fitness-based selection and complex demographic scenarios.</p> <p>Conclusion</p> <p>GenomePop has many interesting characteristics for simulating SNPs or DNA sequences under complex evolutionary and demographic models. These features make it unique with respect to other simulation tools. Namely, the possibility of forward simulation under General Time Reversible (GTR) mutation or GTR×MG94 codon models with intra-codon recombination, arbitrary, user-defined, migration patterns, diploid or haploid models, constant or variable population sizes, etc. It also allows simulation of fitness-based selection under different distributions of mutational effects. Under the 2-allele model it allows the simulation of recombination hot-spots, the definition of different frequencies in different populations, etc. GenomePop can also manage large DNA fragments. In addition, it has a scaling option to save computation time when simulating large sequences and population sizes under complex demographic and evolutionary situations. These and many other features are detailed in its web page <abbrgrp><abbr bid="B1">1</abbr></abbrgrp>.</p