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Genomic selection (GS) is a technology used for genetic improvement, and it has many advantages over phenotype-based selection. There are several statistical models that adequately approach the statistical challenges in GS, such as in linear mixed models (LMMs). An active area of research is the development of software for fitting LMMs mainly used to make genome-based predictions. The lme4 is the standard package for fitting linear and generalized LMMs in the R-package, but its use for genetic analysis is limited because it does not allow the correlation between individuals or groups of individuals to be defined. This article describes the new lme4GS package for R, which is focused on fitting LMMs with covariance structures defined by the user, bandwidth selection, and genomic prediction. The new package is focused on genomic prediction of the models used in GS and can fit LMMs using different variance-covariance matrices. Several examples of GS models are presented using this package as well as the analysis using real data.

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In all breeding programs, the decision about which individuals to select and intermate to form the next selection cycle is crucial. The improvement of genetic stocks requires considering multiple traits simultaneously, given that economic value and net genetic merits depend on many traits; therefore, with the advance of computational and statistical tools and genomic selection (GS), researchers are focusing on multi-trait selection. Selection of the best individuals is difficult, especially in traits that are antagonistically correlated, where improvement in one trait might imply a reduction in other(s). There are approaches that facilitate multi-trait selection, and recently a Bayesian decision theory (BDT) has been proposed. Parental selection using BDT has the potential to be effective in multi-trait selection given that it summarizes all relevant quantitative genetic concepts such as heritability, response to selection and the structure of dependence between traits (correlation). In this study, we applied BDT to provide a treatment for the complexity of multi-trait parental selection using three multivariate loss functions (LF), Kullback-Leibler (KL), Energy Score, and Multivariate Asymmetric Loss (MALF), to select the best-performing parents for the next breeding cycle in two extensive real wheat data sets. Results show that the high ranking lines in genomic estimated breeding value (GEBV) for certain traits did not always have low values for the posterior expected loss (PEL). For both data sets, the KL LF gave similar importance to all traits including grain yield. In contrast, the Energy Score and MALF gave a better performance in three of four traits that were different than grain yield. The BDT approach should help breeders to decide based not only on the GEBV per se of the parent to be selected, but also on the level of uncertainty according to the Bayesian paradigm.

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Abstract Worldwide big cats are at risk of extinction, and anthropogenic factors and natural habitat disturbances represent the biggest threats for their survival. It is essential to know the natural resources use by these predators and the way these big felids can adapt to changes. It is unknown how the puma (Puma concolor) selects and uses resources, what environmental factors determine its presence and how this species is affected by natural disturbances in Mexican tropical forests. This study was performed in the Eden ecological reserve and surroundings, in the North of Quintana Roo, Mexico, an area dominated by tropical semideciduous (medium forest) and secondary forest (acahual). Camera samplings were carried out during 2008, and from 2010 to 2012. Habitat variables, activity patterns and species associations were also spatially and temporally analyzed using achi-squared test and overlapping coefficients. General Linear Models (GLM) were used in order to determine which variables influence the presence of cougars in the study area. Cougars used vegetation and paths in different proportions as the availability of these resources. The years with more changes (P < 0.05) were 2008 and 2011. This predator was active throughout the day, but changed its activity patterns over the years. The cougar was spatio-temporally associated with six mammals and two big terrestrial birds: Pecari tajacu (∆ = 0.52), Meleagris ocellata (∆ = 0.55), Crax rubra (∆ = 0.58), Didelphis sp. (∆ = 0.64), Mazama temama (∆ = 0.66), Leopardus pardalis (∆ = 0.68), Dasypus novemcinctus (∆ = 0.73) and Panthera onca (∆ = 0.87). After testing 90 GLM models, the model with a lower AIC value described the activity patterns of prey and co-predators. The vegetation and water in the reserve were important variables for the cougar. However the variables that determined and modified the presence of the species were activity patterns of co-predators and the potential preys. The factors that negatively affected the presence of the species were fire, human presence, and habitat displacement to less favorable habitats to avoid jaguar. Rev. Biol. Trop. 66(1): 78-90. Epub 2018 March 01.

Resumen Los grandes felinos a nivel mundial se encuentran en peligro de extinción. Los factores antropogénicos y las alteraciones naturales representan una gran presión para su sobrevivencia. Es esencial conocer el efecto de estos sobre los depredadores y cómo los felinos se adaptan y usan los recursos naturales. Se desconoce el modo en que el puma (Puma concolor) selecciona y utiliza recursos, cuáles son los factores ambientales que determinan su presencia y cómo esta especie se ve afectada por alteraciones naturales en los bosques tropicales mexicanos. Este estudio se realizó en la reserva ecológica de El Edén y sus alrededores en el norte de Quintana Roo, México, área dominada por selva tropical semidecidua (selva mediana) y bosque secundario (acahual). Se realizaron muestreos con cámaras durante 2008 y 2010-2012. Las variables de hábitat, patrones de actividad y asociaciones de especies también se analizaron espacial y temporalmente mediante una prueba de chi-cuadrado y coeficientes de traslape. Se utilizaron modelos GLM para determinar qué variables influyen en la presencia de pumas en el área de estudio. El puma utiliza la vegetación y caminos en diferente proporción a la de su disponibilidad. Los años con más cambios (P <0.05) fueron 2008 y 2011. Este depredador está activo durante todo el día, pero cambió sus patrones de actividad durante los años. El puma está asociado espacio-temporalmente con siete mamíferos: Pecari tajacu (Δ = 0.52), Meleagris ocelata (Δ = 0.55), Crax rubra (Δ = 0.58), Didelphis sp. (Δ = 0.64), Mazama temama (Δ = 0.66), Leopardus pardalis (Δ = 0.68), Dasypus novemcinctus (Δ = 0.73) y Panthera onca (Δ = 0.87) y dos grandes aves terrestres. Después de probar 90 modelos GLM, el modelo con un valor menor de AIC es el de patrones de actividad de presas y co-depredadores. La vegetación y la disponibilidad de agua en la reserva son variables importantes para el puma. Sin embargo, las variables que determinan y modifican la presencia de la especie son los patrones de actividad de los co-depredadores y las presas potenciales. Los factores que afectan negativamente la presencia de la especie son el fuego, la presencia humana y el desplazamiento a habitas menos favorables para evadir al jaguar.

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Wildlife density estimates provide an idea of the current state of populations, and in some cases, reflect the conservation status of ecosystems, essential aspects for effective management actions. In Mexico, several regions have been identified as high priority areas for the conservation of species that have some level of risk, like the Yucatan Peninsula (YP), where the country has the largest population of jaguars. However, little is known about the current status of threatened and endangered felids, which coexist in the Northeastern portion of the Peninsula. Our objective was to estimate the wild cats' density population over time at El Eden Ecological Reserve (EEER) and its surrounding areas. Camera trap surveys over four years (2008, 2010, 2011 and 2012) were conducted, and data were obtained with the use of capture-recapture models for closed populations (CAPTURE + MMDM or 1/2 MMDM), and the spatially explicit capture-recapture model (SPACECAP). The species studied were jaguar (Panthera onca), puma (Puma concolor), ocelot (Leopardus pardalis), jaguarundi (Puma yaguaroundi) and margay (Leopardus wiedii). Capture frequency was obtained for all five species and the density for three (individuals/100km2). The density estimated with The Mean Maximum Distance Moved (MMDM), CAPTURE, ranged from 1.2 to 2.6 for jaguars, from 1.7 to 4.3 for pumas and from 1.4 to 13.8 for ocelots. The density estimates in SPACECAP ranged from 0.7 to 3.6 for jaguars, from 1.8 to 5.2 for pumas and 2.1 to 5.1 for ocelots. Spatially explicit capture recapture (SECR) methods in SPACECAP were less likely to overestimate densities, making it a useful tool in the planning and decision making process for the conservation of these species. The Northeastern portion of the Yucatan Peninsula maintains high populations of cats, the EEER and its surrounding areas are valuable sites for the conservation of this group of predators. Rev. Biol.

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Resumen:La estimación de la densidad de fauna silvestre permite tener una idea del estado de salud de las poblaciones y en algunos casos indica el estado de conservación de los ecosistemas. Los métodos de evaluación deben hacer estimaciones no sesgadas, ya que servirán de base para estrategias de conservación de especies clave. Algunas regiones en México han sido identificadas como áreas de alta prioridad para la conservación de especies con cierto nivel de riesgo, como es la Península de Yucatán (PY), donde prevalece la mayor población de jaguares en México. Sin embargo, poco se sabe acerca de la situación actual de los felinos amenazados y en peligro de extinción, como un grupo de especies que conviven en la parte noreste de la Península. Nuestro objetivo fue estimar la densidad de las poblaciones de felinos silvestres a mediano plazo en la Reserva Ecológica El Edén (EEER) y sus alrededores. Se llevaron a cabo muestreos con cámaras-trampa durante cuatro años (2008, 2010, 2011 y 2012), se usaron modelos de captura-recaptura para poblaciones cerradas (CAPTURA + MMDM o VMMDM) y un modelo de C-R espacial-mente explícito (CERC) por medio del paquete SPCACAP para realizar las estimaciones de densidad. Las especies estudiadas fueron: jaguar (Panthera onca),puma (Puma concolor),ocelote (Leopardus pardalis),jaguarundi (Puma yaguaroundi)y tigrillo (Leopardus wiedii).La frecuencia de captura se obtuvo para las cinco especies y la densidad para tres (individuos/100km2). La densidad estimada por medio de MMDM varió entre 1.2 y 2.6 para jaguares, pumas (1.7-4.3) y ocelotes (1.4-13.8). Las estimaciones de la densidad en SPACECAP variaron desde 0.7 hasta 3.6 para jaguares, de 1.8 a 5.2 para pumas y de 2.1 a 5.1 en ocelotes. El método de C-R espacialmente explícito (SECR, SPACECAP) tiene menos probabilidades de sobrestimar la densidad, lo que provee una herramienta útil en el proceso de planificación y toma de decisiones para la conservación de estas especies. La parte noreste de la Península de Yucatán mantiene poblaciones altas de felinos, la REEE y sus alrededores son clave para la conservación de este grupo de depredadores.

Abstract:Wildlife density estimates provide an idea of the current state of populations, and in some cases, reflect the conservation status of ecosystems, essential aspects for effective management actions. In Mexico, several regions have been identified as high priority areas for the conservation of species that have some level of risk, like the Yucatan Peninsula (YP), where the country has the largest population ofjaguars. However, little is known about the current status of threatened and endangered felids, which coexist in the Northeastern portion of the Peninsula. Our objective was to estimate the wild cats' density population over time at El Eden Ecological Reserve (EEER) and its surrounding areas. Camera trap surveys over four years (2008, 2010, 2011 and 2012) were conducted, and data were obtained with the use of capture-recapture models for closed populations (CAPTURE + MMDM or 'V MMDM), and the spatially explicit capture-recapture model (SPACECAP). The species studied were jaguar (Panthera onca),puma (Puma concolor),ocelot (Leopardus pardalis),jaguarundi (Puma yaguaroundi)and margay (Leopardus wiedii).Capture frequency was obtained for all five species and the density for three (individuals/100km2). The density estimated with The Mean Maximum Distance Moved (MMDM), CAPTURE, ranged from 1.2 to 2.6 for jaguars, from 1.7 to 4.3 for pumas and from 1.4 to 13.8 for ocelots. The density estimates in SPACECAP ranged from 0.7 to 3.6 for jaguars, from 1.8 to 5.2 for pumas and 2.1 to 5.1 for ocelots. Spatially explicit capture recapture (SECR) methods in SPACECAP were less likely to overestimate densities, making it a useful tool in the planning and decision making process for the conservation of these species. The Northeastern portion of the Yucatan Peninsula maintains high populations of cats, the EEER and its surrounding areas are valuable sites for the conservation of this group of predators.

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Selection indices are estimates of the net genetic merit of the individual candidates for selection and are calculated based on phenotyping and molecular marker information collected on plants under selection in a breeding program. They reflect the breeding value of the plants and help breeders to choose the best ones for next generation. Rindsel is an R package that calculates phenotypic and molecular selection indices.

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