purgeR: inbreeding and purging in pedigreed populations

SUMMARY: Inbreeding depression and genetic purging are important processes shaping the survivability and evolution of small populations. However, detecting purging is challenging in practice, in part because there are limited tools dedicated to it. I present a new R package to assist population analyses on detection and quantification of the inbreeding depression and genetic purging of biological fitness in pedigreed populations. It includes a collection of methods to estimate different measurements of inbreeding (Wright’s, partial and ancestral inbreeding coefficients) as well as purging parameters (purged inbreeding, and opportunity of purging coefficients). Additional functions are also included to estimate population parameters, allowing to contextualize inbreeding and purging these results in terms of the population demographic history. purgeR is a valuable tool to gain insight into processes related to inbreeding and purging, and to better understand fitness and inbreeding load evolution in small populations. AVAILABILITY AND IMPLEMENTATION: purgeR is an R package available at CRAN, and can be installed via install.packages(“purgeR”). Source code is maintained at a GitLab repository (https://gitlab.com/elcortegano/purgeR). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Evaluación de la purga genética en poblaciones de censo reducido

La depresión consanguínea puede ser decisiva para la extinción de poblaciones de censopequeño. Sin embargo, la consanguinidad también incrementa la selección contra losdeletéreos responsables de dicha depresión. A este incremento de la selección se ledenomina purga genética. Sus consecuencias pueden analizarse utilizando el modelo IP(García-Dorado 2012), que permite predecir la reducción del lastre de consanguinidad yde la depresión consanguínea atribuibles a la purga a través de un coeficiente deconsanguinidad purgado (g) que depende del coeficiente de purga (d).Hasta la fecha se ha publicado una única estima de d para la purga en condiciones nocompetitivas, obtenida en un experimento con Drosophila (Bersabé & García-Dorado2013). Sin embargo, existen evidencias de que d puede ser mayor en las condiciones máscompetitivas de las poblaciones silvestres que en cautividad. Además, es necesarioestimar d en las propias poblaciones amenazadas de interés, donde no es posible el diseñoexperimental pero a menudo se dispone de medidas de la eficacia individual y registrosgenealógicos..

Identificación de Gestos para la Interacción con Sistemas de Realidad Aumentada mediante Seguimiento de Mano

En un mundo cada vez más digitalizado, uno de los grandes retos tecnológicos es adaptar y optimizar la interacción entre persona y máquina. Especialmente en el campo de la Realidad Extendida (XR), una tecnología que en la actualidad es uno de los focos de la innovación y, donde muchos equipos y compañías experimentan e investigan nuevas formas de interacción con el entorno y los artefactos digitales. Por ello, es de especial importancia diseñar interfaces intuitivas y sistemas de interacción usables para los usuarios [1]. En este trabajo se presenta un modelo que permite definir gestos de manera digital con el que se busca agilizar el proceso de identificación de los mismos a partir de secuencias de imágenes capturadas por una cámara. Para evaluar la eficacia y usabilidad del modelo, se han desarrollado herramientas: una para ordenador y otra móvil de Realidad Aumentada (AR) con las que posteriormente se ha experimentado con usuarios. Los voluntarios que han participado en los experimentos afirman que la curva de aprendizaje del sistema de interacción diseñado es baja. Los experimentos realizados concluyen que el sistema diseñado es fiable y que las aplicaciones que lo implementan son usables

Highly pleiotropic variants of human traits are enriched in genomic regions with strong background selection

Recent studies have shown the ubiquity of pleiotropy for variants affecting human complex traits. These studies also show that rare variants tend to be less pleiotropic than common ones, suggesting that purifying natural selection acts against highly pleiotropic variants of large effect. Here, we investigate the mean frequency, effect size and recombination rate associated with pleiotropic variants, and focus particularly on whether highly pleiotropic variants are enriched in regions with putative strong background selection. We evaluate variants for 41 human traits using data from the NHGRI-EBI GWAS Catalog, as well as data from other three studies. Our results show that variants involving a higher degree of pleiotropy tend to be more common, have larger mean effect sizes, and contribute more to heritability than variants with a lower degree of pleiotropy. This is consistent with the fact that variants of large effect and frequency are more likely detected by GWAS. Using data from four different studies, we also show that more pleiotropic variants are enriched in genome regions with stronger background selection than less pleiotropic variants, suggesting that highly pleiotropic variants are subjected to strong purifying selection. From the above results, we hypothesized that a number of highly pleiotropic variants of low effect/frequency may pass undetected by GWAS.Ministerio de Ciencia, Innovación y Universidades | Ref. FPU18/04642Agencia Estatal de Investigación | Ref. PID2020-114426GB-C21Xunta de Galicia | Ref. ED431C 2020-0

Genetic purging in captive endangered ungulates with extremely low effective population sizes

Inbreeding threatens the survival of small populations by producing inbreeding depression, but also exposes recessive deleterious effects in homozygosis allowing for genetic purging. Using inbreeding-purging theory, we analyze early survival in four pedigreed captive breeding programs of endangered ungulates where population growth was prioritized so that most adult females were allowed to contribute offspring according to their fitness. We find evidence that purging can substantially reduce inbreeding depression in Gazella cuvieri (with effective population size Ne = 14) and Nanger dama (Ne = 11). No purging is detected in Ammotragus lervia (Ne = 4), in agreement with the notion that drift overcomes purging under fast inbreeding, nor in G. dorcas (Ne = 39) where, due to the larger population size, purging is slower and detection is expected to require more generations. Thus, although smaller populations are always expected to show smaller fitness (as well as less adaptive potential) than larger ones due to higher homozygosis and deleterious fixation, our results show that a substantial fraction of their inbreeding load and inbreeding depression can be purged when breeding contributions are governed by natural selection. Since management strategies intended to maximize the ratio from the effective to the actual population size tend to reduce purging, the search for a compromise between these strategies and purging could be beneficial in the long term. This could be achieved either by allowing some level of random mating and some role of natural selection in determining breeding contributions, or by undertaking reintroductions into the wild at the earliest opportunity

Estudio epidemiológico en una muestra clínica de mujeres a través del dis

La investigación epidemiológica llevada a cabo en las últimas décadas en nuestro país ha demostrado, de manera inequívoca, la existencia de marcadas diferencias en la morbilidad psicopatológica y en el patrón de conducta de enfermedad desarrollados según el sexo (Vázquez-Barquero, Diez Manrique, Peña, Quintanal y Labrador López, 1986; Herrera, Antonell, Espagnolo, Domenech y Martín, 1987; Herrera, Antonell, Spagnolo y Gispert, 1990). Este hecho, unido a la constatación de que la prevalencia psicopatológica en la mujer es mucho mayor que en el hombre y que el riesgo de padecer un trastorno mental puede ser casi del doble en el sexo femenino (Muñoz, 1979; Herrera et al., 1987; Vázquez-Barquero, Diez Manrique y Peña, 1987), nos hacen plantear la presente investigación con el objetivo de conocer el tipo de desórdenes psicológicos que afectan de forma preferente a la población femenina, objetivo éste enmarcado en un planteamiento metodológico de tipo epidemiológico descriptivo

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125–234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene actionAgencia Estatal de Investigación (AEI) | Ref. PGC2018-095810-B-I00Agencia Estatal de Investigación (AEI) | Ref. PID2020-114426GB-C21Xunta de Galicia | Ref. ED431C 2020-0

Crecimiento corporal, composición proximal del músculo y parámetros hematológicos de juveniles de Colossoma macropomum alimentados con una dieta exclusivamente vegetal en comparación con una dieta con bajo contenido de harina de pescado

The aim of this study was to determine the effect of a vegetable diet compared to a diet containing fishmeal at the commercial level (6%) on body growth, proximal composition of fillets and hematological parameters of juvenil gamitana (Colossoma macropomum). The experiment followed a completely randomized design with two treatments, an exclusively vegetable diet and a diet with low fishmeal content (6%), and three 200 m3 dug earthen ponds as experimental units per treatment. A total of 1200 fish (172.9 g; 19.4 cm) distributed in the six ponds (1 fish/m3) were used. Feeding was done twice a day (08:00 and 16:00) at a daily feeding rate of 2% for 60 days. The water quality parameters were monitored daily and showed constant values and within the comfort range of the species. The exclusively vegetable diet had a similar effect as the fishmeal diet on body growth [final weight 258.9 g, weight gain 86.1 g, supplied feed 128.4 g, feed conversion 1.24, relative growth rate 1.74%/day, factor of condition 1.91, 0% mortality], the proximal composition of fillets [moisture 77.90%, ash 1.39%, protein 18.98%, lipid 0.86%], as well as in the hematological parameters. It is concluded that an exclusively vegetable diet can be used for the rearing of juvenile gamitana, contributing to the sustainability of its production and reduction of feeding costs.El estudio tuvo como objetivo determinar el efecto de una dieta vegetal en comparación con una dieta conteniendo harina de pescado al nivel comercial (6%) sobre el crecimiento corporal, composición proximal del músculo y parámetros hematológicos de juveniles de gamitana (Colossoma macropomum). El experimento siguió un diseño completamente al azar con dos tratamientos, una dieta exclusivamente vegetal y una dieta con bajo contenido de harina de pescado (6%), y tres estanques de tierra excavados de 200 m3 como unidades experimentales por tratamiento. Se trabajó con 1200 peces (172.9 g; 19.4 cm) distribuidos en los seis estanques (1 pez/m3). La alimentación se hizo dos veces al día (08:00 y 16:00) a una tasa de alimentación diaria de 2% durante 60 días. Los parámetros de calidad de agua fueron monitoreados diariamente y mostraron valores constantes y dentro del rango de confort de la especie. La dieta exclusivamente vegetal causó similar efecto que la dieta con harina de pescado sobre el crecimiento corporal [peso final 258.9 g, ganancia de peso 86.1 g, alimento ofrecido 128.4 g, conversión alimenticia 1.24, tasa de crecimiento relativo 1.74%/día, factor de condición 1.91, 0% de mortalidad], la composición proximal del músculo [humedad 77.90%, cenizas 1.39%, proteínas 18.98%, lípidos 0.86%], así como en los parámetros hematológicos. Se concluye que una dieta exclusivamente vegetal puede ser utilizada para la crianza de juveniles de gamitana contribuyendo a la sostenibilidad de su producción y reducción de costos por alimentación