Data and models from multi-model inference of non-random mating from an information theoretic approach

This is a co-submission with Multi-model inference of non-random mating from an information theoretic approach [1]. These data corresponds to the complete simulated data set jointly with the set of models defined for analysing the data. The simulated data set was obtained using the program MateSim [2]. The simulated cases correspond to one-sex competition and mate choice models. For each simulation run, the population frequencies (premating individuals) and the sample of 500 mating pairs were generated randomly for a hypothetical trait with two classes at each sex. Some datasets represent larger population size species (n = 10 000) and the mating process was represented as a sampling with replacement, and the population frequencies were constant over the mating season. The minimum phenotype frequency (MPF) allowed was 0.1. Five different model cases were simulated, namely random mating, female competition with mate choice (with independent or compound parameters) and male competition with mate choice (with independent or compound parameters). Each case was simulated 1000 times. Other datasets represent monogamous species (with large or small population size) and the mating process was without replacement (from the point of view of the available phenotypes). These data sets were used to test the performance of the multi-model inference methodology proposed in [1]. The data may be useful for testing any new/old statistics for measuring sexual selection or assortative mating patterns.Xunta de Galicia | Ref. ED431C2016-037Ministerio de Economía, Industria y Competitividad | Ref. CGL2016-75482-

1LocusSim a mobile-friendly simulator for teaching population genetics

MOTIVATION: Biology students often struggle with the fundamental concepts of evolutionary genetics, including genetic drift, mutation and selection. To address this problem, 1LocusSim was developed to simulate the interaction of different factors, such as population size, mutation, selection and dominance, to study their effect on allelic frequency during evolution. With 1LocusSim, students can compare theoretical results with simulation outputs and solve and analyze different problems of population genetics. The 1LocusSim web has a responsive design which means that it has been specifically designed to be used on smartphones. RESULTS: To demonstrate its use, I review the classical overdominance model of population genetics and highlight a characteristic that is often not explicitly stated. Specifically, it is emphasized that the equilibrium of the model does not depend on the homozygous selection coefficients but rather on the ratio of the selection coefficients. This is already clear from the classical formula but maybe not so much for students. Also it implies that the equilibrium can be expressed solely in terms of the dominance coefficient h. To verify this theoretical prediction, I utilize the simulator and calculate the equilibrium for the well-known case of sickle cell anemia. By utilizing this tool, students can learn at their own pace and convenience, anywhere and anytime. AVAILABILITY IMPLEMENTATION: 1LocusSim if freely available at https://1LocusSim-biosdev.pythonanywhere.com/. Website implemented under the Bottle micro web-framework for Python, with all major browsers supported. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.Xunta de Galicia | Ref. ED431C 2020/05Universidade de Vigo/CISU

Unifying quantification methods for sexual selection and assortative mating using information theory

Sexual selection plays a crucial role in modern evolutionary theory, offering valuable insight into evolutionary patterns and species diversity. Recently, a comprehensive definition of sexual selection has been proposed, defining it as any selection that arises from fitness differences associated with nonrandom success in the competition for access to gametes for fertilization. Previous research on discrete traits demonstrated that nonrandom mating can be effectively quantified using Jeffreys (or symmetrized Kullback-Leibler) divergence, capturing information acquired through mating influenced by mutual mating propensities instead of random occurrences. This novel theoretical framework allows for detecting and assessing the strength of sexual selection and assortative mating. In this study, we aim to achieve two primary objectives. Firstly, we demonstrate the seamless alignment of the previous theoretical development, rooted in information theory and mutual mating propensity, with the aforementioned definition of sexual selection. Secondly, we extend the theory to encompass quantitative traits. Our findings reveal that sexual selection and assortative mating can be quantified effectively for quantitative traits by measuring the information gain relative to the random mating pattern. The connection of the information indices of sexual selection with the classical measures of sexual selection is established. Additionally, if mating traits are normally distributed, the measure capturing the underlying information of assortative mating is a function of the square of the correlation coefficient, taking values within the non-negative real number set [0, +∞). It is worth noting that the same divergence measure captures information acquired through mating for both discrete and quantitative traits. This is interesting as it provides a common context and can help simplify the study of sexual selection patternsXunta de Galicia | Ref. ED431C 2020/05Agencia Estatal de Investigación | Ref. PID2022-137935NB-I00Universidade de Vigo/CISU

Simulation of Genomes: A Review

There is an increasing role of population genetics in human genetic research linking empirical observations with hypotheses about sequence variation due to historical and evolutionary causes. In addition, the data sets are increasing in size, with genome-wide data becoming a common place in many empirical studies. As far as more information is available, it becomes clear that simplest hypotheses are not consistent with data. Simulations will provide the key tool to contrast complex hypotheses on real data by generating simulated data under the hypothetical historical and evolutionary conditions that we want to contrast. Undoubtedly, developing tools for simulating large sequences that at the same time allow simulate natural selection, recombination and complex demography patterns will be of great interest in order to better understanding the trace left on the DNA by different interacting evolutionary forces. Simulation tools will be also essential to evaluate the sampling properties of any statistics used on genome-wide association studies and to compare performance of methods applied at genome-wide scales. Several recent simulation tools have been developed. Here, we review some of the currently existing simulators which allow for efficient simulation of large sequences on complex evolutionary scenarios. In addition, we will point out future directions in this field which are already a key part of the current research in evolutionary biology and it seems that it will be a primary tool in the future research of genome and post-genomic biology

Evidence of recombination within human alpha-papillomavirus

BACKGROUND: Human papillomavirus (HPV) has a causal role in cervical cancer with almost half a million new cases occurring each year. Presence of the carcinogenic HPV is necessary for the development of the invasive carcinoma of the genital tract. Therefore, persistent infection with carcinogenic HPV causes virtually all cervical cancers. Some aspects of the molecular evolution of this virus, as the putative importance of recombination in its evolutionary history, are an opened current question. In addition, recombination could also be a significant issue nowadays since the frequency of co-infection with more than one HPV type is not a rare event and, thus, new recombinant types could be currently being generated. RESULTS: We have used human alpha-PV sequences from the public database at Los Alamos National Laboratory to report evidence that recombination may exist in this virus. A model-based population genetic approach was used to infer the recombination signal from the HPV DNA sequences grouped attending to phylogenetic and epidemiological information, as well as to clinical manifestations. Our results agree with recently published ones that use a different methodology to detect recombination associated to the gene L2. In addition, we have detected significant recombination signal in the genes E6, E7, L2 and L1 at different groups, and importantly within the high-risk type HPV16. The method used has recently been shown to be one of the most powerful and reliable procedures to detect the recombination signal. CONCLUSION: We provide new support to the recent evidence of recombination in HPV. Additionally, we performed the recombination estimation assuming the best-fit model of nucleotide substitution and rate variation among sites, of the HPV DNA sequence sets. We found that the gene with recombination in most of the groups is L2 but the highest values were detected in L1 and E6. Gene E7 was recombinant only within the HPV16 type. The topic deserves further study because recombination is an important evolutionary mechanism that could have high impact both in pharmacogenomics (i.e. on the influence of genetic variation on the response to drugs) and for vaccine development

Remoción de nitrógeno, fósforo y producción de biomasa de Scenedesmus sp en agua residual domestica

RESUMEN: Las aguas residuales domésticas se han utilizado como sustrato para la producción de biomasa de microalgas y eliminación de nutrientes. El tratamiento biológico con microalgas fotosintéticas proporciona aireación, reduciendo los costos de operación, el riesgo de volatilización de los contaminantes y proporciona oxígeno a las bacterias para la degradación de compuestos orgánicos. En este estudio se aisló una microalga a partir de aguas naturales y fue identificada como Scenedesmus sp. Se realizó un diseño experimental usando agua residual sintética con diferentes concentraciones de nitrógeno (40, 90 y 150 mg / L), fósforo (4, 15 y 50 mg / L) y la microalga aislada. Cada ensayo se inoculó con 1x106 células/ml bajo 16 horas de iluminación a 50-μmol m-2 s-1 por 7 días a 120 rpm. Se tomaron muestras a 0, 3, 5 y 7 días para determinar el crecimiento de microalgas y la concentración de nitratos, amonio y fósforo. El mismo tratamiento se realizó utilizando agua residual domestica real. Las aguas sintéticas de baja y media concentración tuvieron mayores porcentajes de remoción, entre 50-60% para el nitrógeno y 40-70% para el fósforo, con un crecimiento máximo de 1x107 células/ml. En el agua residual real, la remoción fue del 65% para el fósforo y el 80% para el nitrógeno. Estos resultados sugieren Scenedesmus sp podría ser utilizada para tratar agua residual doméstica, mejorando la eliminación de nutrientes y obteniendo biomasa para otros fines.ABSTRACT: Domestic wastewater (DW) has been used as a substrate for both microalgae biomass production and nutrient removal. Biological treatment with photosynthetic microalgae provides aeration, reducing operating costs and the risk of volatilization of contaminants. It also provides oxygen to the bacteria for degradation of organic compounds. In this study, a microalga was isolated and identified as Scenedesmus sp. An experimental trial was performed using synthetic wastewater with different concentrations of N (40, 90 and 150 mg/L) and P (4, 15 and 50 mg/L). Each assay was inoculated with 1x106 cells/ml under 16h of continuous light at 50-μmol m-2 s-1 at and 120 rpm for 7 days. Samples were taken at 0, 3, 5 and 7 days to determine the growth of microalgae and the concentration of nitrates, ammonium and phosphorus. The same treatment was carried out using real DW. Synthetic water of low and medium concentration had higher removal percentages. These were between 50 and 60 for nitrogen and 40 and 70 for phosphorus, with a maximum growth of 1x107 cells /ml. For real DW, the removal was 65% for phosphorus and 80% for nitrogen. These results suggest Scenedesmus sp could be used to treat DW, enhancing nutrient removal and obtaining biomass for other purposes

0.13-µm CMOS tunable transconductor based on the body-driven gain boosting technique with application in Gm-C filters

We present a low-voltage low-power CMOS tunable transconductor exploiting body gain boosting to increase the small-signal output resistance. As a distinctive feature, the proposed scheme allows the OTA transconductance to be tuned via the current biasing the gain-boosting circuit. The proposed transconductor has been designed in a 0.13-µm CMOS technology and powered from a 1.2-V supply. To show a possible application, a 0.5-MHz tunable third order Chebyshev low pass filter suitable for the Ultra Low Power Bluetooth Standard has been designed. The filter simulations show that all the requirements of the chosen standard are met, with good performance in terms of linearity, noise and power consumption

Pharmacological and Nonpharmacological Therapeutic Strategies Based on the Pathophysiology of Acute and Chronic Spinal Cord Injury

Spinal cord injury (SCI) induces a series of anatomic and physiological disorders which have severe repercussions on neural function. SCI is classified chronologically into an acute (primary and secondary phase) and a chronic phase. The primary phase results directly from the initial trauma and is comprised of disturbances in neural tissue (mainly axons), blood vessels, and spinal shock. Secondary injury results from a series of time-dependent pathophysiological changes, beginning in the first minutes after SCI and lasting days and weeks. This phase is characterized by biochemical and immunological alterations in the injury site and periphery, leading to neuronal over-excitation, apoptosis, and axonal demyelination. In chronic stages, the pathophysiology consists of disturbances in fiber organization, oligodendrocyte apoptosis, fibroglial scar formation, and cyst formation, leading to parenchymal alterations such as syringomyelia and hydromyelia hindering the possibility for functional basal axonal regeneration. This chapter will review a wide range of pharmacological and nonpharmacological therapeutic strategies in preclinical and clinical phases, each targeting different pathological mechanisms of SCI in acute and chronic stages of SCI; taking into account limitations, advances, scope, and new trends. The chapter focuses on the general aspects of SCI pathophysiology, pharmacological and nonpharmacological treatments acute and chronic stages of SCI

Portable multispectral imaging system based on Raspberry Pi

Purpose In this work, the authors aim to present a compact low-cost and portable spectral imaging system for general purposes. The developed system provides information that can be used for a fast in situ identification and classification of samples based on the analysis of captured images. The connectivity of the instrument allows a deeper analysis of the images in an external computer. Design/methodology/approach The wavelength selection of the system is carried out by light multiplexing through a light-emitting diode panel where eight wavelengths covering the spectrum from ultraviolet (UV) to near-infrared region (NIR) have been included. The image sensor used is a red green blue – infrared (RGB-IR) micro-camera controlled by a Raspberry Pi board where a basic image processing algorithm has been programmed. It allows the visualization in an integrated display of the reflectance and the histogram of the images at each wavelength, including UV and NIRs. Findings The prototype has been tested by analyzing several samples in a variety of applications such as detection of damaged, over-ripe and sprayed fruit, classification of different type of plastic materials and determination of properties of water. Originality/value The designed system presents some advantages as being non-expensive and portable in comparison to other multispectral imaging systems. The low-cost and size of the camera module connected to the Raspberry Pi provides a compact instrument for general purposes.Project CTQ2013-44545-R from the Ministry of Economy and Competitiveness (Spain)Junta de Andalucía (Proyecto de Excelencia P10-FQM-5974)European Regional Development Funds (ERDF

An integrated approach to infer the mechanisms of mate choice for size

Size-assortative mating and sexual selection on size are common across species. Since both may be a result of mate choice, mate choice based on size should also be a widespread process. This behaviour is, however, rarely studied directly and thus the biological causes that determine size-based mate choice are poorly understood. To address this, we studied the size-based mate choice in an intertidal snail, Echinolittorina malaccana, that has been used as a model to understand this process. Previous studies, assuming a quantitative Gaussian mating preference function, have inferred that mate choice in this snail is caused by a size similarity mechanism (males prefer to mate with females slightly larger than themselves). To further test and quantify this proposed mechanism, we conducted mate choice experiments with alternative designs (single, male and multiple choice) in the laboratory and compared the results to mate choice data observed in natural populations. This integrated approach allowed us to elucidate the mechanism of mate choice by evaluating alternative mating models that best fitted the observed data of various designs. Results confirmed the similarity-based mechanism but showed deviations at extreme size classes. The single choice design indicated that mate choice was exercised during one-on-one maleefemale interactions, but the strength of mate choice increased with the presence of additional individuals (males in the male choice design, and both males and females in the multiplechoice design). Multiple-choice experiments are, therefore, the most valuable and useful design to infer how males choose mates in the wild, as they best mimic the natural scenario and the results are the most similar to those observed in natural populations. To elucidate the mechanisms causing this male choice for particular female sizes, the next steps are to identify the genetic basis as well as potential physiological benefits associated with choosing slightly larger females.Xunta de Galicia | Ref. ED431C 2020-05Ministerio de Economía, Industria y Competitividad | Ref. CGL2016-75482-